[ { "id": "authors:7y46s-pe313", "collection": "authors", "collection_id": "7y46s-pe313", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101214-081744371", "type": "article", "title": "Transposable element insertions have strongly affected human evolution", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Comparison of a full collection of the transposable element (TE) sequences of vertebrates with genome sequences shows that the human genome makes 655 perfect full-length matches. The cause is that the human genome contains many active TEs that have caused TE inserts in relatively recent times. These TE inserts in the human genome are several types of young Alus (AluYa5, AluYb8, AluYc1, etc.). Work in many laboratories has shown that such inserts have many effects including changes in gene expression, increases in recombination, and unequal crossover. The time of these very effective changes in the human lineage genome extends back about 4 million years according to these data and very likely much earlier. Rapid human lineage-specific evolution, including brain size is known to have also occurred in the last few million years. Alu insertions likely underlie rapid human lineage evolution. They are known to have many effects. Examples are listed in which TE sequences have influenced human-specific genes. The proposed model is that the many TE insertions created many potentially effective changes and those selected were responsible for a part of the striking human lineage evolution. The combination of the results of these events that were selected during human lineage evolution was apparently effective in producing a successful and rapidly evolving species.", "doi": "10.1073/pnas.1014330107", "pmcid": "PMC2993358", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2010-11-16", "series_number": "46", "volume": "107", "issue": "46", "pages": "19945-19948" }, { "id": "authors:44pvx-hrf17", "collection": "authors", "collection_id": "44pvx-hrf17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-151137509", "type": "article", "title": "Climate Change and the Integrity of Science", "author": [ { "family_name": "Gleick", "given_name": "P. H.", "clpid": "Gleick-P-H" }, { "family_name": "Anderson", "given_name": "D. J.", "orcid": "0000-0001-6175-3872", "clpid": "Anderson-D-J" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Roberts", "given_name": "John D.", "clpid": "Roberts-J-D" } ], "abstract": "We are deeply disturbed by the recent escalation of political assaults on scientists in general and on climate scientists in particular. All citizens should understand some basic scientific facts. There is always some uncertainty associated with scientific conclusions; science\nnever absolutely proves anything. When someone says that society should wait until scientists are absolutely certain before taking any action, it is the same as saying society should never take action. For a problem as potentially catastrophic as climate change, taking no action poses\na dangerous risk for our planet.", "doi": "10.1126/science.328.5979.689", "pmcid": "PMC5125622", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2010-05-07", "series_number": "5979", "volume": "328", "issue": "5979", "pages": "689-690" }, { "id": "authors:hzk28-wqd47", "collection": "authors", "collection_id": "hzk28-wqd47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRInpre08", "type": "article", "title": "Idiosyncratic evolution of conserved eukaryote proteins that are similar in sequence to archaeal or bacterial proteins", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Sequence comparisons have been made between the proteins of 571 prokaryote species including 46 archaea and 525 bacteria and the set of human proteins. Highly conserved eukaryotic proteins are often strikingly similar in sequence to archaeal and bacterial proteins. Yet in many cases similarity to archaeal proteins is not correlated to the similarity to bacterial proteins. In these comparisons there are hundreds of eukaryote\nproteins that match well archeal proteins, but do not match recognizably to bacterial\nproteins, while thousands of proteins match well to bacterial proteins but not\nrecognizably to archeal proteins. Forty percent of the 21,440 human proteins that\nsignificantly match prokaryote proteins are in this extreme idiosyncratic category. These\nrelationships have been preserved over billions of years since the last common ancestor\nor sharing of protein genes between prokaryotes and eukaryotes. For each of the 21,440\nmembers of this set of human proteins (that make significant matches to any of the 1.8\nmillion proteins in this set of prokaryote species protein libraries) it is certain that each\nprotein has important functions both in prokaryotes and eukaryotes and the precursor\nproteins have been important in the precursor species of both. That is the only\nexplanation for the preservation of amino acid sequence similarity for the billions of\nyears since the last common ancestor or period of sharing of proteins. Comparisons were\nmade between the proteins of Arabidopsis thaliana and Saccharomyces cerevisiae to the\nproteins of the 571 prokaryote species. The results agreed with the human comparisons\nindicating that the conclusions apply to eukaryotes generally.", "doi": "10.1038/npre.2008.1752.1", "publisher": "Nature Publishing Group", "publication": "Nature Precedings", "publication_date": "2008" }, { "id": "authors:wyzg5-0m859", "collection": "authors", "collection_id": "wyzg5-0m859", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas06", "type": "article", "title": "Almost all human genes resulted from ancient duplication", "author": [ { "family_name": "Britten", "given_name": "Roy", "clpid": "Britten-R-J" } ], "abstract": "Results of protein sequence comparison at open criterion show a very large number of relationships that have, up to now, gone unreported. The relationships suggest many ancient events of gene duplication. It is well known that gene duplication has been a major process in the evolution of genomes. A collection of human genes that have known functions have been examined for a history of gene duplications detected by means of amino acid sequence similarity by using BLASTp with an expectation of two or less (open criterion). Because the collection of genes in build 35 includes sets of transcript variants, all genes of known function were collected, and only the longest transcription variant was included, yielding a 13,298-member library called KGMV (for known genes maximum variant). When all lengths of matches are accepted, >97% of human genes show significant matches to each other. Many form matches with a large number of other different proteins, showing that most genes are made up from parts of many others as a result of ancient events of duplication. To support the use of the open criterion, all of the members of the KGMV library were twice replaced with random protein sequences of the same length and average composition, and all were compared with each other with BLASTp at expectation two or less. The set of matches averaged 0.35% of that observed for the KGMV set of proteins.", "doi": "10.1073/pnas.0510007103", "pmcid": "PMC1748171", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2006-12-12", "series_number": "50", "volume": "103", "issue": "50", "pages": "19027-19032" }, { "id": "authors:rwhe7-k0409", "collection": "authors", "collection_id": "rwhe7-k0409", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas05", "type": "article", "title": "The majority of human genes have regions repeated in other human genes", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Amino acid sequence comparisons have been made between all of 25,193 human proteins with each of the others by using BLAST software (National Center for Biotechnology Information) and recording the results for regions that are significantly related in sequence, that is, have an expectation of <1x10^-3. The results are presented for each amino acid as the number of identical or similar amino acids matched in these aligned regions. This approach avoids summing or dealing directly with the different regions of any one protein that are often related to different numbers and types of other proteins. The results are presented graphically for a sample of 140 proteins. Relationships are not observed for 26.5% of the 12,728,866 amino acids. The average number of related amino acids is 36.5 for the majority (73.5%) that show relationships. The median number of recognized relationships is ~3 for all of the amino acids, and the maximum number is 718. The results demonstrate the overwhelming importance of gene regional duplication forming families of proteins with related domains and show the variety of the resulting patterns of relationship. The magnitude of the set of relationships leads to the conclusion that the principal process by which new gene functions arise has been by making use of preexisting genes.", "doi": "10.1073/pnas.0501008102", "pmcid": "PMC555776", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2005-04-12", "series_number": "15", "volume": "102", "issue": "15", "pages": "5466-5470" }, { "id": "authors:09way-4c761", "collection": "authors", "collection_id": "09way-4c761", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas04", "type": "article", "title": "Coding sequences of functioning human genes derived entirely from mobile element sequences", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Among all of the many examples of mobile elements or \"parasitic sequences\" that affect the function of the human genome, this paper describes several examples of functioning genes whose sequences have been almost completely derived from mobile elements. There are many examples where the synthetic coding sequences of observed mRNA sequences are made up of mobile element sequences, to an extent of 80% or more of the length of the coding sequences. In the examples described here, the genes have named functions, and some of these functions have been studied. It appears that each of the functioning genes was originally formed from mobile elements and that in some process of molecular evolution a coding sequence was derived that could be translated into a protein that is of some importance to human biology. In one case (AID7C), the coding sequence is 99% made up of a cluster of Alu sequences. In another example, the gene BNIP3 coding sequence is 97% made up of sequences from an apparent human endogenous retrovirus. The Syncytin gene coding sequence appears to be made from an endogenous retrovirus envelope gene.", "pmcid": "PMC534736", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2004-11-30", "series_number": "48", "volume": "101", "issue": "48", "pages": "16825-16830" }, { "id": "authors:krttt-ewf66", "collection": "authors", "collection_id": "krttt-ewf66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas03", "type": "article", "title": "Majority of divergence between closely related DNA samples is due to indels", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Rowen", "given_name": "Lee", "clpid": "Rowen-L" }, { "family_name": "Williams", "given_name": "John", "clpid": "Williams-J" }, { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" } ], "abstract": "It was recently shown that indels are responsible for more than twice as many unmatched nucleotides as are base substitutions between samples of chimpanzee and human DNA. A larger sample has now been examined and the result is similar. The number of indels is approximate to1/12th of the number of base substitutions and the average length of the indels is 36 nt, including indels up to 10 kb. The ratio (R-u) of unpaired nucleotides attributable to indels to those attributable to substitutions is 3.0 for this 2 million-nt chimp DNA sample compared with human. There is similar evidence of a large value of R-u for sea urchins from the polymorphism of a sample of Strongylocentrotus purpuratus DNA (Ru = 3-4). Other work indicates that similarly, per nucleotide affected, large differences are seen for indels in the DNA polymorphism of the plant Arabidopsis thaliana (R-u = 51). For the insect Drosophila melanogaster a high value of R-u (4.5) has been determined. For the nematode Caenorhabditis elegans the polymorphism data are incomplete but high values of R-u are likely. Comparison of two strains of Escherichia coli O157:H7 shows a preponderance of indels. Because these six examples are from very distant systematic groups the implication is that in general, for alignments of closely related DNA, indels are responsible for many more unmatched nucleotides than are base substitutions. Human genetic evidence suggests that indels are a major source of gene defects, indicating that indels are a significant source of evolutionary change.", "doi": "10.1073/pnas.0330964100", "pmcid": "PMC153612", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2003-04-15", "series_number": "8", "volume": "100", "issue": "8", "pages": "4661-4665" }, { "id": "authors:bhvmk-qhr93", "collection": "authors", "collection_id": "bhvmk-qhr93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas02", "type": "article", "title": "Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Five chimpanzee bacterial artificial chromosome (BAC) sequences (described in GenBank) have been compared with the best matching regions of the human genome sequence to assay the amount and kind of DNA divergence. The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels. The gaps in alignment are present in about equal amounts in the chimp and human sequences. They occur equally in repeated and nonrepeated sequences, as detected by REPEATMASKER (http://ftp.genome.washington.edu/RM/RepeatMasker.html).", "doi": "10.1073/pnas.172510699", "pmcid": "PMC129726", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2002-10-15", "series_number": "21", "volume": "99", "issue": "21", "pages": "13633-13635" }, { "id": "authors:agccr-dhq69", "collection": "authors", "collection_id": "agccr-dhq69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CAMpnas00", "type": "article", "title": "A sea urchin genome project: Sequence scan, virtual map, and additional resources", "author": [ { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Mahairas", "given_name": "Gregory", "clpid": "Mahairas-G" }, { "family_name": "Rast", "given_name": "Jonathan P.", "clpid": "Rast-J-P" }, { "family_name": "Martinez", "given_name": "Pedro", "clpid": "Martinez-P" }, { "family_name": "Biondi", "given_name": "Ted R.", "clpid": "Biondi-T-R" }, { "family_name": "Swartzell", "given_name": "Steven", "clpid": "Swartzell-S" }, { "family_name": "Wallace", "given_name": "James C.", "clpid": "Wallace-J-C" }, { "family_name": "Poustka", "given_name": "Albert J.", "clpid": "Poustka-A-J" }, { "family_name": "Livingston", "given_name": "Brian T.", "clpid": "Livingston-B-T" }, { "family_name": "Wray", "given_name": "Gregory A.", "clpid": "Wray-G-A" }, { "family_name": "Ettensohn", "given_name": "Charles A.", "clpid": "Ettensohn-C-A" }, { "family_name": "Lehrach", "given_name": "Hans", "clpid": "Lehrach-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Hood", "given_name": "Leroy", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "abstract": "Results of a first-stage Sea Urchin Genome Project are summarized here. The species chosen was Strongylocentrotus purpuratus, a research model of major importance in developmental and molecular biology. A virtual map of the genome was constructed by sequencing the ends of 76,020 bacterial artificial chromosome (BAC) recombinants (average length, 125 kb). The BAC-end sequence tag connectors (STCs) occur an average of 10 kb apart, and, together with restriction digest patterns recorded for the same BAC clones, they provide immediate access to contigs of several hundred kilobases surrounding any gene of interest. The STCs survey >5% of the genome and provide the estimate that this genome contains approx 27,350 protein-coding genes. The frequency distribution and canonical sequences of all middle and highly repetitive sequence families in the genome were obtained from the STCs as well. The 500-kb Hox gene complex of this species is being sequenced in its entirety. In addition, arrayed cDNA libraries of >105 clones each were constructed from every major stage of embryogenesis, several individual cell types, and adult tissues and are available to the community. The accumulated STC data and an expanding expressed sequence tag database (at present including >12,000 sequences) have been reported to GenBank and are accessible on public web sites.", "doi": "10.1073/pnas.160261897", "pmcid": "PMC16896", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2000-08-15", "series_number": "17", "volume": "97", "issue": "17", "pages": "9514-9518" }, { "id": "authors:xjndz-50d87", "collection": "authors", "collection_id": "xjndz-50d87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111207-130103463", "type": "article", "title": "EST analysis of gene expression in early cleavage-stage sea urchin embryos", "author": [ { "family_name": "Lee", "given_name": "Youn-Ho", "clpid": "Lee-Youn-Ho" }, { "family_name": "Huang", "given_name": "Guyang Matthew", "clpid": "Huang-Guyang-Matthew" }, { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Graham", "given_name": "Geoffrey", "clpid": "Graham-G" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Hood", "given_name": "Leroy", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented 'housekeeping' proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1999-09", "series_number": "17", "volume": "126", "issue": "17", "pages": "3857-3867" }, { "id": "authors:4bphr-syr51", "collection": "authors", "collection_id": "4bphr-syr51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-073654390", "type": "article", "title": "SM37, a skeletogenic gene of the sea urchin embryo linked to the SM50 gene", "author": [ { "family_name": "Lee", "given_name": "Youn-Ho", "clpid": "Lee-Youn-Ho" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The genomic DNA region that contains the SM50 gene also included a second gene that appeared to encode another skeletogenic matrix protein. The two genes were linked at a distance of about 12 kb. Based on the molecular weight of the implied protein the gene was termed SM37. The SM37 protein included a long tandem sequence of short glycine-rich repeats that was similar to the glycine-rich repeats included in the SM50 protein and several other skeletal matrix proteins, although the sequence of SM37 repeat was distinct. The overall structure of the SM37 protein was similar to SM50 as well. However, SM37 was only about 30% identical in amino acid sequence to SM50, and coding region probes behaved as a single copy sequence under standard conditions. The SM37 gene included the same cis-regulatory elements as the SM50 gene, although in a different order with respect to transcription. This gene was regulated coordinately with SM50 during development, and like SM50 was expressed exclusively in skeletogenic mesenchyme lineages.", "doi": "10.1046/j.1440-169X.1999.413429.x", "issn": "0012-1592", "publisher": "Japanese Society of Developmental Biologists", "publication": "Development, Growth & Differentiation", "publication_date": "1999-06", "series_number": "3", "volume": "41", "issue": "3", "pages": "303-312" }, { "id": "authors:n68h4-y9f12", "collection": "authors", "collection_id": "n68h4-y9f12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121025-093551154", "type": "article", "title": "Microsatellite Loci in Wild-Type and Inbred Strongylocentrotus purpuratus", "author": [ { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Leahy", "given_name": "Patrick S.", "clpid": "Leahy-P-S" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Strongylocentrotus purpuratus,a major research model in developmental molecular biology, has been inbred through six generations of sibling matings. Though viability initially decreased, as described earlier, the inbred line now consists of healthy, fertile animals. These are intended to serve as a genomic resource in which the level of polymorphism is decreased with respect to wildS. purpuratus.To genotype the inbred animals eight simple sequence genomic repeats were isolated, in context, and PCR primers were generated against the flanking single-copy sequences. Distribution and polymorphism of these regions of the genome were studied in the genomes of 27 wild individuals and in a sample of the inbred animals at F2 and F3 generations. All eight regions were polymorphic, though to different extents, and their homozygosity was increased by inbreeding as expected. The eight markers suffice to identify unambiguously the cellular DNA of any wild or F3S. purpuratus individual.", "doi": "10.1006/dbio.1999.9224", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1999-04-15", "series_number": "2", "volume": "208", "issue": "2", "pages": "255-264" }, { "id": "authors:60bvx-7qw53", "collection": "authors", "collection_id": "60bvx-7qw53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas98c", "type": "article", "title": "Underlying assumptions of developmental models", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "These 10 obvious propositions make a model of the specification of form, intended to expose underlying assumptions of developmental biology for examination and future experimentation. (I) The control of development is by means of local interactions, rather than global control mechanisms. (II) A macromolecule near a specific site will bind by mass action. (III) Starting with a precursor cell, all cells are assembled automatically by specifically binding macromolecules. (IV) At the surface of cells are specific adhesion sites that determine how all cells bind to each other. (V) An organism will assemble automatically from parts (macromolecules, structures, and cells) specified by nuclear control factors. (VI) The nuclear control factors in each cell are from precursor cells and factors derived by signaling from other cells. (VII) The macromolecules that determine specific binding, cell adhesion, and signaling are controlled by nuclear control factors, and in a grand feedback the cell adhesion and signaling systems determine the nuclear factor patterns. (VIII) The embryonic precursor cells for organs, termed \"precursor groups,\" are linked by adhesion and signaling relationships. (IX) The precursor groups include precursors for regions of an organ and boundary cells between regions having few cell types, growing without additional specific cell-to-cell relationships. (X) Organs are held together by cell adhesion in functional relationships. Thus the form and function of the organism is specified entirely by local control mechanisms. Without global control systems, information for form is in the genes for structural proteins, adhesion molecules, control factors, signaling molecules, and their control regions.", "doi": "10.1073/pnas.95.16.9372", "pmcid": "PMC21345", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1998-08-04", "series_number": "16", "volume": "95", "issue": "16", "pages": "9372-9377" }, { "id": "authors:eyb3g-rdm60", "collection": "authors", "collection_id": "eyb3g-rdm60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas98b", "type": "article", "title": "Precise sequence complementarity between yeast chromosome ends and two classes of just-subtelomeric sequences", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The terminal regions (last 20 kb) of Saccharomyces cerevisiae chromosomes universally contain blocks of precise sequence similarity to other chromosome terminal regions. The left and right terminal regions are distinct in the sense that the sequence similarities between them are reverse complements. Direct sequence similarity occurs between the left terminal regions and also between the right terminal regions, but not between any left ends and right ends. With minor exceptions the relationships range from 80% to 100% match within blocks. The regions of similarity are composites of familiar and unfamiliar repeated sequences as well as what could be considered \"single-copy\" (or better \"two-copy\") sequences. All terminal regions were compared with all other chromosomes, forward and reverse complement, and 768 comparisons are diagrammed. It appears there has been an extensive history of sequence exchange or copying between terminal regions. The subtelomeric sequences fall into two classes. Seventeen of the chromosome ends terminate with the Y' repeat, while 15 end with the 800-nt \"X2\" repeats just adjacent to the telomerase simple repeats. The just-subterminal repeats are very similar to each other except that chromosome 1 right end is more divergent.", "pmcid": "PMC34494", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1998-05-26", "series_number": "11", "volume": "95", "issue": "11", "pages": "5906-5912" }, { "id": "authors:ws9qj-waq93", "collection": "authors", "collection_id": "ws9qj-waq93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas98a", "type": "article", "title": "A gravitational diffusion model without dark matter", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "In this model, without dark matter, the flat rotation curves of galaxies and the mass-to-light ratios of clusters of galaxies are described quantitatively. The hypothesis is that the agent of gravitational force is propagated as if it were scattered with a mean free path of approx 5 kiloparsecs. As a result, the force between moderately distant masses, separated by more than the mean free path, diminishes as the inverse first power of the distance, following diffusion equations, and describes the flat rotation curves of galaxies. The force between masses separated by <1 kiloparsec diminishes as the inverse square of distance. The excess gravitational force (ratio of 1/r:1/r2) increases with the scale of structures from galaxies to clusters of galaxies. However, there is reduced force at great distances because of the approx 12 billion years that has been available for diffusion to occur. This model with a mean free path of approx 5 kiloparsecs predicts a maximum excess force of a few hundredfold for objects the size of galactic clusters a few megaparsecs in size. With only a single free parameter, the predicted curve for excess gravitational force vs. size of structures fits reasonably well with observations from those for dwarf galaxies through galactic clusters. Under the diffusion model, no matter is proposed in addition to the observed baryons plus radiation and thus the proposed density of the universe is only a few percent of that required for closure.", "pmcid": "PMC19838", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1998-03-31", "series_number": "7", "volume": "95", "issue": "7", "pages": "3351-3355" }, { "id": "authors:s57q9-hj522", "collection": "authors", "collection_id": "s57q9-hj522", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160323-091824746", "type": "article", "title": "Mobile elements inserted in the distant past have taken on important functions", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Current evidence on the long-term evolutionary effect of insertion of sequence elements is reviewed. There are three criteria for inclusion of an example: (i) the element was inserted far in the past and thus the event is not a transient mutation; (ii) the element is a member of a large group of similar sequences; (iii) the element now serves a useful function. There are 21 examples from Drosophila, sea urchin, human and mouse genomes that meet these criteria. Taken together, these examples show that the insertion of sequence elements in the genome has been a significant source of regulatory variation in evolution.", "doi": "10.1016/S0378-1119(97)00399-5", "issn": "0378-1119", "publisher": "Elsevier", "publication": "Gene", "publication_date": "1997-12-31", "series_number": "1-2", "volume": "205", "issue": "1-2", "pages": "177-182" }, { "id": "authors:zbaax-4ab31", "collection": "authors", "collection_id": "zbaax-4ab31", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas96", "type": "article", "title": "DNA sequence insertion and evolutionary variation in gene regulation", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Current evidence on the long-term evolutionary effect of insertion of sequence elements into gene regions is reviewed, restricted to cases where a sequence derived from a past insertion participates in the regulation of expression of a useful gene. Ten such examples in eukaryotes demonstrate that segments of repetitive DNA or mobile elements have been inserted in the past in gene regions, have been preserved, sometimes modified by selection, and now affect control of transcription of the adjacent gene. Included are only examples in which transcription control was modified by the insert. Several cases in which merely transcription initiation occurred in the insert were set aside. Two of the examples involved the long terminal repeats of mammalian endogenous retroviruses. Another two examples were control of transcription by repeated sequence inserts in sea urchin genomes. There are now six published examples in which Alu sequences were inserted long ago into human gene regions, were modified, and now are central in control/enhancement of transcription. The number of published examples of Alu sequences affecting gene control has grown threefold in the last year and is likely to continue growing. Taken together, all of these examples show that the insertion of sequence elements in the genome has been a significant source of regulatory variation in evolution.", "pmcid": "PMC38434", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1996-09-03", "series_number": "18", "volume": "93", "issue": "18", "pages": "9374-9377" }, { "id": "authors:vkq1x-79736", "collection": "authors", "collection_id": "vkq1x-79736", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160412-104335578", "type": "article", "title": "Cases of Ancient Mobile Element DNA Insertions That Now Affect Gene Regulation", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "There is no doubt that mobile elements are a major source of mutation and that in many cases insertions cause changes in the expression of genes, but a question remains open. What has the long-term effect of these processes been? The data collected here show that in many eukaryotes, segments of repetitive DNA (mobile elements) that have been inserted in the past in regions of many eukaryote genes have been preserved by selection and now affect the transcriptional control of these specific genes. At least five of the examples are considered to be solid cases demonstrating this history. There are a number of significant but less compelling sets of evidence that support the concept that the insertion of mobile elements in gene regions could be a major source of regulatory variation in evolution.", "doi": "10.1006/mpev.1996.0003", "issn": "1055-7903", "publisher": "Elsevier", "publication": "Molecular Phylogenetics and Evolution", "publication_date": "1996-02", "series_number": "1", "volume": "5", "issue": "1", "pages": "13-17" }, { "id": "authors:gjpxe-r9569", "collection": "authors", "collection_id": "gjpxe-r9569", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160331-103438066", "type": "article", "title": "Sea Urchin Genes Expressed in Activated Coelomocytes Are Identified by Expressed Sequence Tags. Complement Homologues and Other Putative Immune Response Genes Suggest Immune System Homology Within the Deuterostomes", "author": [ { "family_name": "Smith", "given_name": "L. Courtney", "clpid": "Smith-L-C" }, { "family_name": "Chang", "given_name": "Lily", "clpid": "Chang-Lily" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "To identify some of the genes expressed in LPS-activated coelomocytes, we sequenced randomly chosen clones from a directionally constructed cDNA library to produce a set of expressed sequence tags (ESTs). Deduced amino acid sequences from 307 ESTs were compared with known protein sequences in GenBank, and significant matches to approximately 30% of the clones were identified. Eighty-nine clones matched to 55 different proteins, including several putative immune effector proteins. In this work, we show the first identification of an invertebrate homologue of a vertebrate C component. Another EST matches to several short consensus repeats that are characteristic of a variety of proteins, including CR/regulatory proteins and clotting factors. Additional putative immune effector genes include 1) a Kazal-type protease inhibitor that may function to inactivate bacterial proteases, 2) a C-type lectin similar to echinoidin, and 3) a serine protease with similarities to thrombin, elastase, haptoglobin, and plasmin. Other EST categories include 1) cell surface proteins and receptors, 2) proteins involved in signaling systems, 3) lysosomal and secreted proteins, 4) cytoskeletal and cytoskeletal modifying proteins, 5) general cell function proteins, 6) proteins with unknown function, and 7) ESTs without significant matches, 25 with open reading frames. Many of the ESTs identified in this study represent the types of genes expected to be used in lower deuterostome immune functions.", "issn": "0022-1767", "publisher": "American Association of Immunologists", "publication": "Journal of Immunology", "publication_date": "1996-01-15", "series_number": "2", "volume": "156", "issue": "2", "pages": "593-602" }, { "id": "authors:bhzzh-yz509", "collection": "authors", "collection_id": "bhzzh-yz509", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120215-152338740", "type": "article", "title": "Cis-regulatory control of the SM50 gene, an early marker of skeletogenic lineage specification in the sea urchin embryo", "author": [ { "family_name": "Makabe", "given_name": "Kazuhiro W.", "clpid": "Makabe-Kazuhiro-W" }, { "family_name": "Kirchhamer", "given_name": "Carmen V.", "clpid": "Kirchhamer-C-V" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The SM50 gene encodes a minor matrix protein of the sea urchin embryo spicule. We carried out a detailed functional analysis of a cis-regulatory region of this gene, extending 440 bp upstream and 120 bp downstream of the transcription start site, that had been shown earlier to confer accurate skeletogenic expression of an injected expression vector. The distal portion of this fragment contains elements controlling amplitude of expression, while the region from \u2212200 to +105 contains spatial control elements that position expression accurately in the skeletogenic lineages of the embryo. A systematic mutagenesis analysis of this region revealed four adjacent regulatory elements, viz two copies of a positively acting sequence (element D) that are positioned just upstream of the transcription start site; an indispensable spatial control element (element C) that is positioned downstream of the start site; and further downstream, a second positively acting sequence (element A). We then constructed a series of synthetic expression constructs. These contained oligonucleotides representing normal and mutated versions of elements D, C, and A, in various combinations. We also changed the promoter of the SM50 gene from a TATA-less to a canonical TATA box form, without any effect on function. Perfect spatial regulation was also produced by a final series of constructs that consisted entirely of heterologous enhancers from the CyIIIa gene, the SV40 early promoter, and synthetic D, C, and A elements. We demonstrate that element C exercises the primary spatial control function of the region we analyzed. We term this a 'locator' element. This differs from conventional 'tissue-specific enhancers' in that while it is essential for expression, it has no transcriptional activity on its own, and it requires other, separable, positive regulatory elements for activity. In the normal configuration these ancillary positive functions are mediated by elements A and D. Only positively acting control elements were observed in the SM50 regulatory domain throughout this analysis.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1995-07", "series_number": "7", "volume": "121", "issue": "7", "pages": "1957-1970" }, { "id": "authors:p43ay-5qt51", "collection": "authors", "collection_id": "p43ay-5qt51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160317-080034463", "type": "article", "title": "Developmental Utilization of SpP3A1 and SpP3A2: Two Proteins Which Recognize the Same DNA Target Site in Several Sea Urchin Gene Regulatory Regions", "author": [ { "family_name": "Zeller", "given_name": "Robert W.", "clpid": "Zeller-R-W" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "SpP3A1 and SpP3A2 are DNA-binding proteins that interact specifically with the same target sites in the regulatory domains of the Strongylocentrotus purpuratus CyIIIa gene and also of several other known genes. In this work we used antibodies raised against recombinant P3A1 and P3A2 to quantitate these transcription factors in eggs and in the nuclear compartments of embryos of various stages. Both proteins are present in unfertilized eggs, and both enter the embryonic nuclei early in development, but only P3A2 remains present in nuclei at functional concentrations beyond the early gastrula stage. Combined with earlier measurements of P3A site binding at cleavage stages, these measurements show that P3A1 would be replaced by P3A2 at target sites in genes regulated by these factors.", "doi": "10.1006/dbio.1995.1196", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1995-07", "series_number": "1", "volume": "170", "issue": "1", "pages": "75-82" }, { "id": "authors:1ek9n-m0q14", "collection": "authors", "collection_id": "1ek9n-m0q14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160311-071745501", "type": "article", "title": "SpGCF1, a Sea Urchin Embryo DNA-Binding Protein, Exists as Five Nested Variants Encoded by a Single mRNA", "author": [ { "family_name": "Zeller", "given_name": "Robert W.", "clpid": "Zeller-R-W" }, { "family_name": "Coffman", "given_name": "James A.", "clpid": "Coffman-J-A" }, { "family_name": "Harrington", "given_name": "Michael G.", "orcid": "0000-0002-7923-8032", "clpid": "Harrington-M-G" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Several Strongylocentrotus purpuratus gene cis-regulatory regions contain asymmetric C_4 sequences which are core elements of target sites for a specific DNA-protein interaction. Blastula stage nuclear extract contains five proteins which specifically bind to these target sites, resulting in a characteristic pattern of complexes in gel mobility shift assays. We used automated affinity chromatography to purify a protein which binds to these sites and have isolated the corresponding cDNA. This protein, SpGCF1, is a novel sea urchin DNA-binding protein with no overall homology to proteins reported in the databases currently available. The DNA-binding domain of this protein was identified by a deletion analysis. As demonstrated both for protein translated in vitro and for bacterial protein expressed from a cDNA clone, a single SpGCF1 mRNA serves as a template for the synthesis of five DNA-binding polypeptides. We show that these five polypeptides are most likely produced by differential usage of a nested set of AUG start codons in the SpGCF1 cDNA and thus contain variable amounts of a proline-rich N-terminal domain. Since proline-rich regions often serve as transcriptional activation domains, the five SpGCF1 proteins apparently possess different \"activation potentials.\"", "doi": "10.1006/dbio.1995.1181", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1995-06", "series_number": "2", "volume": "169", "issue": "2", "pages": "713-727" }, { "id": "authors:sxpf1-twc53", "collection": "authors", "collection_id": "sxpf1-twc53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151223-141227669", "type": "article", "title": "Maternal and embryonic provenance of a sea urchin embryo transcription factor, SpZ12-1", "author": [ { "family_name": "Wang", "given_name": "D. G.", "clpid": "Wang-D-G" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" } ], "abstract": "SpZ12-1 is a zinc-finger transcription factor. Previous work has indicated that this factor functions late in embryogenesis as a spatial transcriptional repressor. We show here that this factor is present in significant quantities even in unfertilized egg cytoplasm, and in similar quantities in mesenchyme blastula-stage embryo cytoplasm. Taken together with earlier measurements of Calzone and associates, our observations indicate that SpZ12-1 enters the embryonic nuclei between late cleavage and mesenchyme blastula stages. A low-prevalence mRNA encoding SpZ12-1 is also present throughout development. Translation of this mRNA could, however, easily account for the complete complement of SpZ12-1 protein in the embryo, as estimated from its DNA binding activity. SpZ12-1 probably functions at several developmental stages and is evidently of both maternal and embryonic provenance.", "issn": "1053-6426", "publisher": "Springer", "publication": "Molecular Marine Biology and Biotechnology", "publication_date": "1995-06", "series_number": "2", "volume": "4", "issue": "2", "pages": "148-153" }, { "id": "authors:7tpwa-ap205", "collection": "authors", "collection_id": "7tpwa-ap205", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151223-141054015", "type": "article", "title": "Lipopolysaccharide activates the sea urchin immune system", "author": [ { "family_name": "Smith", "given_name": "L. Courtney", "clpid": "Smith-L-C" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Profilin is a small, actin-binding protein that functions at the intersection of signal transduction and cytoskeletal modifications. Increases in the number of profilin messages per cell correlate with sea urchin coelomocyte activation in response to injury. Here we show that coelomocytes respond to immune challenge from lipopolysaccharide with significant elevations in profilin transcripts per coelomocyte.", "doi": "10.1016/0145-305X(95)00009-I", "issn": "0145-305X", "publisher": "Elsevier", "publication": "Developmental and Comparative Immunology", "publication_date": "1995-05", "series_number": "3", "volume": "19", "issue": "3", "pages": "217-224" }, { "id": "authors:466yy-vkh32", "collection": "authors", "collection_id": "466yy-vkh32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120216-102559113", "type": "article", "title": "SpZ12-1, a negative regulator required for spatial control of the territory-specific CyIIIa gene in the sea urchin embryo", "author": [ { "family_name": "Wang", "given_name": "David G.-W.", "clpid": "Wang-David-G-W" }, { "family_name": "Kirchhamer", "given_name": "Carmen V.", "clpid": "Kirchhamer-C-V" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The CyIIIa cytoskeletal actin gene of the sea urchin Strongylocentrotus purpuratus is activated in late cleavage and expressed exclusively in the aboral ectoderm territory of the embryo. Previous gene transfer studies defined a 2.3 kb cis-regulatory region that is necessary and sufficient for correct temporal and spatial expression of a CyIIIa. CAT fusion gene. In this paper, a negative regulatory element within this region was identified that is required for repression of the CyIIIa gene in skeletogenic mesenchyme cells. The repression mediated by this regulatory element takes place after initial territorial specification. A cDNA clone encoding a DNA-binding protein with twelve Zn fingers (SpZ12-1) was isolated by probing an expression library with this cis-element. Deletion analysis of the SpZ12-1 protein confirmed that a DNA-binding domain is located within the Zn finger region. SpZ12-1 is the only DNA-binding protein in embryo nuclear extract that interacts with the specific cis-target sites required for repression of CyIIIa.CAT in skeletogenic mesenchyme and is likely to be the trans factor that mediates this repression.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1995-04-01", "series_number": "4", "volume": "121", "issue": "4", "pages": "1111-1122" }, { "id": "authors:q0vhy-3jh68", "collection": "authors", "collection_id": "q0vhy-3jh68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141203-135120757", "type": "article", "title": "A multimerizing transcription factor of sea urchin embryos capable of looping DNA", "author": [ { "family_name": "Zeller", "given_name": "Robert W.", "clpid": "Zeller-R-W" }, { "family_name": "Griffith", "given_name": "Jack D.", "clpid": "Griffith-J-D" }, { "family_name": "Moore", "given_name": "James G.", "clpid": "Moore-J-G" }, { "family_name": "Kirchhamer", "given_name": "Carmen V.", "clpid": "Kirchhamer-C-V" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "SpGCF1 is a recently cloned sea urchin transcription factor that recognizes target sites in several different sea urchin genes. We find that in gel-shift experiments this factor is able to multimerize. A quantitative simulation of the gel-shift results suggests that SpGCF1 molecules that are bound to DNA target sites may also bind to one another, thus associating several DNA probe molecules. SpGCF1 might therefore be able to loop DNA molecules bearing its target sites at distant locations. We demonstrate this prediction by electron microscopy, and using the well-characterized cis-regulatory domain of the CyIIIa cytoskeletal actin gene, we show that the loop conformations predicted from the known SpGCF1 target site locations are actually formed in vitro. We speculate that the multimerization of this factor in vivo may function to bring distant regions of extended regulatory domains into immediate proximity so that they can interact with one another.", "doi": "10.1073/pnas.92.7.2989", "pmcid": "PMC42344", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1995-03-28", "series_number": "7", "volume": "92", "issue": "7", "pages": "2989-2993" }, { "id": "authors:shf6p-wsx80", "collection": "authors", "collection_id": "shf6p-wsx80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151223-111751365", "type": "article", "title": "Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer", "author": [ { "family_name": "Springer", "given_name": "Mark S.", "clpid": "Springer-M-S" }, { "family_name": "Tusneem", "given_name": "Nadeem A.", "clpid": "Tusneem-N-A" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Phylogenetic relationships, rates of evolution, and codon usage were investigated in a family of retrotransposons (SURL elements) found in echinoids. The phylogeny of SURL element reverse transcriptase sequences from 10 echinoid species clearly shows the phylogenetic signature of the host taxa as well as paralogous sequences that diverged prior to speciation events. Two subfamilies (1 and 5) of SURL element reverse transcriptase sequences are recognized that diverged prior to the radiation of the Echinometridae. Comparisons of synonymous versus nonsynonymous substitutions indicate that SURL elements have been active in echinoid genomes and have evolved under purifying selection for millions of years. Rates of synonymous substitution for reverse transcriptase are similar to rates of single-copy DNA evolution and to rates of synonymous substitution for the H3 and H4 histone genes, contradicting the assumption that rates of evolution are accelerated in retrotransposons. Finally, codon usage in SURL elements is biased for codons ending in A or U relative to 42 sea urchin nuclear genes. Biased codon usage is sometimes cited as evidence for horizontal transfer, but in the case of SURL elements this bias occurs in spite of a long history of vertical transmission rather than because of horizontal transfer.", "issn": "0737-4038", "publisher": "Oxford University Press", "publication": "Molecular Biology and Evolution", "publication_date": "1995-03", "series_number": "2", "volume": "12", "issue": "2", "pages": "219-230" }, { "id": "authors:nrndt-pm144", "collection": "authors", "collection_id": "nrndt-pm144", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas95", "type": "article", "title": "Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "A gypsy/Ty3-class retrotransposon (Cer1) is integrated in the DNA of Caenorhabditis elegans chromosome III. It is 8865 nt in length and has 492-nt long terminal repeats that are identical in DNA sequence. There is an exceptionally long (6819 nt) open reading frame uninterrupted by frameshift mutations in the period since the insertion, which must therefore have been rather recent. Alignment with other gypsy-class elements and with retroviruses indicates that an env gene occupies the 3' 1.2 kb of the open reading frame. A search through GenBank has uncovered two additional gypsy-class elements from C. elegans that are very closely related in DNA sequence to this insert and are transcribed. Since gypsy of Drosophila has been shown to be an infectious element, it is possible that retrovirus-like gypsy elements are active in C. elegans.", "pmcid": "PMC42789", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1995-01-17", "series_number": "2", "volume": "92", "issue": "2", "pages": "599-601" }, { "id": "authors:9n6f1-pjg71", "collection": "authors", "collection_id": "9n6f1-pjg71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151222-135249234", "type": "article", "title": "Gypsy/Ty3-class retrotransposons integrated in the DNA of herring, tunicate, and echinoderms", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "McCormack", "given_name": "Thomas J.", "clpid": "McCormack-T-J" }, { "family_name": "Mears", "given_name": "Tamara L.", "clpid": "Mears-T-L" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Eight new examples of retrotransposons of the Gypsy/Ty3 class have been identified in marine species. A 525-nt pol gene-coding region was amplified using degenerate primers from highly conserved regions and has extended the range of recognition of Gypsy/Ty3 far beyond those previously known. The following matrix shows the percentage AA divergence of the translations of this segment of the pol gene coding region. Spr2 Strongylocentrotus purpuratus, sea urchin 39 Por2 Pisaster ochraceus, starfish 46 45 Cprl Clupea pallasi, herring 51 52 41 Cirl Ciona intestinalis, tunicate bar52 49 49 55 P. orchraceus, starfish 55 60 60 62 62 Spr3 S. purpuratus, sea urchin 55 61 60 63 61 24 Tgrl* Tripneustes gratilla, sea urchin 56 61 60 63 58 26 27 Lvrl* Lytechinus variegatus, sea urchin 57 62 60 64 62 27 10 29 Sprl* S. purpuratus 58 61 62 65 61 15 27 30 31 Spr4 S. purpuratus 72 72 74 75 72 73 72 72 73 72 Por3 P. ochraceus The underlines separate three groups of retrotransposons that can be recognized on the basis of this amino acid sequence. The new upper group shows surprising amino acid sequence similarity among members from the DNA of herring, sea urchin, starfish, and a tunicate. For example, the herring element differs by only 41 % from the Ciona element and 46% from the sea urchin element. The group between the lines includes members close to previously known elements (marked by asterisks) and has so far been found only in sea urchins. The two upper groups differ from each other by 55\u201360% and yet members of both groups (e.g., Sprl and Spr2) are integrated into the DNA of one species-S. purpuratus. Below the lower underline is listed the only known representative of a very distant group, which occurs in starfish DNA. In spite of large divergence, amino acid sequence comparisons indicate that all of the elements shown in the array are members of the LTR-containing class of retrotransposons that includes Gypsy of Drosophila and Ty3 of yeast. Of all known mobile elements this class shows the closest sequence similarity to retroviruses and has the same arrangement of genes as simpler retroviruses.", "doi": "10.1007/BF00166592", "issn": "0022-2844", "publisher": "Springer Verlag", "publication": "Journal of Molecular Evolution", "publication_date": "1995-01", "series_number": "1", "volume": "40", "issue": "1", "pages": "13-24" }, { "id": "authors:zjabz-1bx55", "collection": "authors", "collection_id": "zjabz-1bx55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151223-092605241", "type": "article", "title": "The sea urchin profilin gene is specifically expressed in mesenchyme cells during gastrulation", "author": [ { "family_name": "Smith", "given_name": "L. Courtney", "clpid": "Smith-L-C" }, { "family_name": "Harrington", "given_name": "Michael G.", "orcid": "0000-0002-7923-8032", "clpid": "Harrington-M-G" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Eggs and embryos of the purple sea urchin (Strongylocentrotus purpuratus) contain profilin that is partly supplied from maternal sources and partly produced by the gastrula. The maternal profilin protein content is about 13 \u03bcM and it persists in the embryo at least through gastrulation. Transcript quantitation from probe excess titrations show that very few profilin gene transcripts are present in the embryo during cleavage, but that they increase at the onset of gastrulation. By in situ hybridization, the newly synthesized profilin transcripts are localized in mesenchyme cells. Profilin gene expression increases when mesenchyme cells initiate migration and filopodial extension and retraction. We show that there are three isoforms of maternal profilin protein produced from the single copy gene during oogenesis. However, the blastula stage embryo only produces the major isoform, whereas the acidic isoform is produced in the early stages of gastrulation and the basic isoform appears by the end of gastrulation. Based on transcript prevalence and protein production rates, our calculations indicate that the amount of new protein produced in the mesenchyme cells in 12 hr is at maximum <2% of that supplied from maternal sources. Because of the large amount of maternally supplied profilin present in the egg and embryo, we suggest that it may be used in the cytokinetic processes of cleavage. Alternatively, because of the small amount of embryonically produced profilin, we suggest that it may function in the cytoskeletal shape changes required for filopodial extension and motility in the mesenchyme cells during gastrulation.", "doi": "10.1006/dbio.1994.1216", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1994-08", "series_number": "2", "volume": "164", "issue": "2", "pages": "463-474" }, { "id": "authors:rz98e-h1972", "collection": "authors", "collection_id": "rz98e-h1972", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151223-095605667", "type": "article", "title": "Complexity and organization of DNA-protein interactions in the 5\u2032-regulatory region of an endoderm-specific marker gene in the sea urchin embryo", "author": [ { "family_name": "Yuh", "given_name": "Chiou-Hwa", "clpid": "Yuh-Chiou-Hwa" }, { "family_name": "Ransick", "given_name": "Andrew", "clpid": "Ransick-A" }, { "family_name": "Martinez", "given_name": "Pedro", "clpid": "Martinez-P" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "This study concerns the organization of sites of specific DNA/protein interaction within the regulatory domain of the Endo16 gene of Strongylocentrotus purpuratus. Earlier work had displayed a complex pattern of expression of this gene during embryogenesis. Endo16 transcripts are confined to the definitive vegetal plate in blastula stage embryos; at gastrula stage this gene is expressed throughout the archenteron, but later only in the midgut. In this work we exploited the exceptional experimental accessibility of the sea urchin embryo, with respect to both functional assays of gene regulatory systems and to characterization of transcription factors, in order to approach a complete description of potential Endo16 regulatory interactions. Accurate expression of an Endo16 fusion gene was obtained with a 2200-nucleotide (nt) upstream fragment of the gene. We present a map locating high specificity target sites for DNA-binding proteins within the 2200-nt Endo16 regulatory domain, and an assessment of the complexity of the set of putative Endo16 transcription factors that we have been able to recover from 24-h (blastula stage) nuclear extract. Protein binding sites were initially mapped by gel shift reactions carried out on nested sets of end-labeled restriction fragments, and then to finer resolution by oligonucleotide gel shift competitions. Thirty-eight sites of high specificity DNA-protein interaction were thus identified. Appropriate oligonucleotides were then used for partial purification of the DNA-binding proteins by affinity chromatography. DNA-binding proteins specific for each target site were identified by molecular weight, using southwestern blotting procedures and two-dimensional gel shift separations, and by directly renaturing and reacting with oligonucleotide probes specific proteins that had been resolved by SDS-PAGE from selected affinity column fractions. A complete series of gel shift cross-competitions amongst the target sites was carried out. We conclude that nine different protein factors are bound at unique sites within the Endo16 regulatory domain. Multiple target sites for five other proteins account for the remaining binding site locations. The target sites appear to be organized in a sequence of clusters, focused on the unique factors. The high complexity of the Endo16 gene regulatory system may be characteristic for genes that are spatially regulated in early embryonic development.", "doi": "10.1016/0925-4773(94)90088-4", "issn": "0925-4773", "publisher": "Elsevier", "publication": "Mechanisms of Development", "publication_date": "1994-08", "series_number": "2", "volume": "47", "issue": "2", "pages": "165-186" }, { "id": "authors:pvf5e-2aj91", "collection": "authors", "collection_id": "pvf5e-2aj91", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas94b", "type": "article", "title": "Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The primate Alu interspersed repeats can be subdivided into classes on the basis of shared nucleotides at a set of diagnostic positions. Each of the classes of Alu sequences is apparently the result of past retrotransposition of transcripts of highly conserved class-specific source genes that differed from each other at the diagnostic positions. The nucleotides at the majority of positions are identical among the source genes and therefore were identical among all of the Alu sequences at the time of their insertion. These CONSBI (conserved before insertion) positions are useful because the changes that have occurred after insertion are recognizable and the divergence resulting from nucleotide substitutions, insertions, and deletions is informative. The divergence of Alu sequences at the CONSBI positions is a measure of the time since a class was inserted. The greatest majority of Alu sequences are in one class (identified as class II), and it is particularly suitable for such examination, since nearly full-length sequences are now known for nearly a thousand members of this class. The average divergence of class II members indicates that the class has an average age of about 40 million years. The distribution in divergence of class II accurately fits a sum of two Poisson distributions. The implication is that class II Alu sequences were derived from two massive past events of insertion of many Alu sequences. In this model the younger subset of class II sequences (corresponding to about 300,000 copies in the genome) has an average divergence of 5% at CONSBI positions. The older set of class II sequences (corresponding to about 150,000 genomic copies) has a 9% average divergence. Based on the drift rate of primate DNA sequences, the events of insertion probably occurred 30-50 million years ago. The goodness of the fit to the Poisson distribution indicates that no significant number of members of class II have been inserted since 30 million years ago.", "pmcid": "PMC44155", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1994-06-21", "series_number": "13", "volume": "91", "issue": "13", "pages": "6148-6150" }, { "id": "authors:s89ww-sg651", "collection": "authors", "collection_id": "s89ww-sg651", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas94a", "type": "article", "title": "Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Mutations have been examined in the 1500 interspersed Alu repeats of human DNA that have been sequenced and are nearly full length. There is a set of particular changes at certain positions that rarely occur (termed suppressed changes) compared to the average of identical changes of identical nucleotides in the rest of the sequence. The suppressed changes occur in positions that are clustered together in what appear to be sites for protein binding. There is a good correlation of the suppression in different positions, and therefore the joint probability of absence of mutation at many pairs of such positions is significantly higher than that expected at random. The suppression of mutation appears to result from selection that is not due to requirements for Alu sequence replication. The implication is that hundreds of thousands of Alu sequences have sequence-dependent functions in the genome that are selectively important for primates. In a few known cases Alu inserts have been adapted to function in the regulation of gene transcription.", "pmcid": "PMC44123", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1994-06-21", "series_number": "13", "volume": "91", "issue": "13", "pages": "5992-5996" }, { "id": "authors:j83ss-h2c67", "collection": "authors", "collection_id": "j83ss-h2c67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151223-111411934", "type": "article", "title": "Repeated Sequence Target Sites for Maternal DNA-Binding Proteins in Genes Activated in Early Sea Urchin Development", "author": [ { "family_name": "Anderson", "given_name": "Roger", "clpid": "Anderson-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "This communication concerns a very highly conserved inverted repeat sequence element that serves as a target site for a sea urchin maternal DNA-binding factor. The maternal factor is present in relatively large amounts in unfertilized eggs, but is about 100\u00d7 less prevalent per embryo in 24-hr embryo nuclear extract. The inverted repeat target site is found in the regulatory domain of the CyIIIa cytoskeletal actin gene and also in two upstream genes encoding transcriptions factors that bind to a functionally important cis-regulatory element of the CyIIIa gene. There are about 460 copies of the inverted repeat target site per genome. About 15% of these sites occur in a nested arrangement together with a second inverted repeat that binds another previously characterized maternal transcription factor. This arrangement is the same as that which occurs in the CyIIIa gene, and it may be of regulatory significance with respect to activation of certain genes in oogenesis and early embryogenesis.", "doi": "10.1006/dbio.1994.1119", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1994-05", "series_number": "1", "volume": "163", "issue": "1", "pages": "11-18" }, { "id": "authors:jnb1r-mpg86", "collection": "authors", "collection_id": "jnb1r-mpg86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121025-095620092", "type": "article", "title": "Development of sibling inbred sea urchins: Normal embryogenesis, but frequent postembryonic malformation, arrest and lethality", "author": [ { "family_name": "Leahy", "given_name": "Patrick S.", "clpid": "Leahy-P-S" }, { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Knox", "given_name": "Melinda A.", "clpid": "Knox-M-A" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Inbred lines of Strongylocentrotus purpuratus descended from a single pair of wild animals were constructed by sibling mating. We describe results from a systematic series of crosses in which eggs from F2 and from F3 females were fertilized respectively with sperm from their sibling males. Observations were also made on self-fertilized cultures derived from several naturally occurring hermaphrodites. Morphological development, survival efficiency, and expression of three territorial embryonic markers were assayed in the embryos developing from these crosses. Unexpectedly, out of > 90 controlled crosses, we observed no developmental failures whatsoever, up to the end of embryogenesis (i.e., onset of feeding) that could be attributed to homozygous, zygotically acting recessive genes. However, during postembryonic larval development, lethality, morphological malformation, and arrest are observed in inbred cultures at a high frequency. The incidence of these zygotic developmental failures is such that it appears that there is at least one recessive genetic defect affecting larval development per haploid parental genome. The relative imperviousness of the basic embryonic process to defects arising from homozygosity is consistent with other evidence implying that territorial specification in sea urchin embryogenesis is controlled by maternally rather than zygotically expressed gene products.", "doi": "10.1016/0925-4773(94)90012-4", "issn": "0925-4773", "publisher": "Elsevier", "publication": "Mechanisms of Development", "publication_date": "1994-03", "series_number": "3", "volume": "45", "issue": "3", "pages": "255-268" }, { "id": "authors:r53nn-mkc46", "collection": "authors", "collection_id": "r53nn-mkc46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121023-153918127", "type": "article", "title": "Ligand-dependent stimulation of introduced mammalian brain receptors alters spicule symmetry and other morphogenetic events in sea urchin embryos", "author": [ { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Smith", "given_name": "L. Courtney", "clpid": "Smith-L-C" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Zygotes of S. purpuratus were injected with synthetic mRNAs encoding rodent brain neurotransmitter receptors, and specific developmental phenotypes were produced on addition to the sea water of the respective ligands. Most of these experiments were carried out with a mouse serotonin receptor (5HT-R) mRNA, though exactly comparable results were obtained with a rat muscarinic acetylcholine receptor (MAChR) mRNA; these receptors are expected to couple to the same endogenous signal transduction system. We show by whole mount in situ hybridization that the injected mRNAs diffuse to all of the early blastomeres, and that they are translated in vivo. Three specific phenotypes were reproducibly observed. The most severe, occurring at highest levels of injected mRNA, was a cleavage arrest phenotype in which no overtly differentiated cells ever appear, though the embryos remain alive for at least 72 h. A gastrular arrest (GA) phenotype is generated in appreciable fractions of embryos developing from eggs injected with lower levels of mRNA. In GA embryos the blastocoel is filled with disorganized mesenchyme cells, including pigment cells and skeletogenic cells; there is no archenteron; and the entire ectoderm expresses an oral ectoderm cell surface marker. The least severe phenotype that we recognized displays an altered arrangement of spiculogenic foci (RSE phenotype), generating a ring of extra spicules that are properly positioned with respect to the animal/vegetal axis, but that lack any reference to the oral/aboral axis. However, use of cytological and molecular markers demonstrates that RSE embryos retain normal spatial patterns of aboral and oral ectoderm. They develop a fully formed archenteron, but fail to form either a stomodaeum or a ciliated band. RSE embryos can be produced in embryos expressing the 5HT-R by exposure to serotonin, beginning as late as 12 h postfertilization (pf). All of the morphogenetic processes affected in RSE embryos depend in normal embryos on intercellular interactions occurring at the blastula-gastrula stages of development.", "doi": "10.1016/0925-4773(94)90051-5", "issn": "0925-4773", "publisher": "Elsevier", "publication": "Mechanisms of Development", "publication_date": "1994-01", "series_number": "1", "volume": "45", "issue": "1", "pages": "31-47" }, { "id": "authors:4gz71-yjk69", "collection": "authors", "collection_id": "4gz71-yjk69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121024-131525401", "type": "article", "title": "The Embryonic Ciliated Band of the Sea Urchin, Strongylocentrotus purpuratus Derives from Both Oral and Aboral Ectoderm", "author": [ { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The ciliated band of the Strongylocentrotus purpuratus embryo consists of a columnar epithelium, 3-5 cells wide, which gives rise to a small number of neuroblasts. It arises late in development, as a border separating the squamous epithelial cells of the oral and aboral ectoderm. To determine the lineage origins of this structure, we performed double labeling experiments at the 2-cell stage and the 16-cell stage, which were designed to reveal clonal boundaries in the ciliated band. The ciliated band forms in a region of the ectoderm derived from descendants of the following blastomeres: No, VO, Na1u, Na2u, right and left NL1u, and right and left NL2u. In contrast to the lineage contributions of the embryonic territories established early in development, lineage origins of the ciliated band are variable. Specification of the ciliated band thus depends on intercellular interaction rather than lineage.", "doi": "10.1006/dbio.1993.1313", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1993-12", "series_number": "2", "volume": "160", "issue": "2", "pages": "369-376" }, { "id": "authors:zkg79-6m393", "collection": "authors", "collection_id": "zkg79-6m393", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151222-160117074", "type": "article", "title": "Whole mount in situ hybridization shows Endo 16 to be a marker for the vegetal plate territory in sea urchin embryos", "author": [ { "family_name": "Ransick", "given_name": "Andrew", "clpid": "Ransick-A" }, { "family_name": "Ernst", "given_name": "Susan", "clpid": "Ernst-S-G" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "We have used whole mount in situ hybridization to analyze the pattern of expression of the gene Endo 16 in S. purpuratus embryos. The mRNA is first detectable at 18 h post-fertilization in the cytoplasm of blastomeres derived from the Veg2 6th cleavage tier. The number of Endo 16 positive cells increases gradually through the beginning of gastrulation, and these cell numbers are in agreement with estimates of the number of cells that should be in the vegetal plate at these stages. We conclude that Endo 16 expression is indeed an early vegetal plate marker and that this gene is expressed by all Veg2 tier derivatives while they are part of the vegetal plate. The progressive regionalization of Endo 16 expression that occurs in normal embryos is also seen in lithium chloride induced exogastrulae, leading to the conclusion that genetic regulation of endoderm differentiation is programmed into the vegetal plate cells once they have been specified. Finally, we report a reproducible phenomenon seen in cultures of LiCl exogastrulae, in which the tips of the everted archenterons fuse, followed by the induction of supernumerary pigment cells.", "doi": "10.1016/0925-4773(93)90001-E", "issn": "0925-4773", "publisher": "Elsevier", "publication": "Mechanisms of Development", "publication_date": "1993-08", "series_number": "3", "volume": "42", "issue": "3", "pages": "117-124" }, { "id": "authors:ryjpv-hhm76", "collection": "authors", "collection_id": "ryjpv-hhm76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MINmbc93", "type": "article", "title": "Species-specific inhibition of fertilization by a peptide derived from the sperm protein bindin", "author": [ { "family_name": "Minor", "given_name": "Joseph E.", "clpid": "Minor-J-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The sperm protein bindin is responsible for the species-specific adhesion of the sperm to the egg. The regions of the bindin molecule responsible for forming the contact between the sperm and the egg were investigated by measuring the ability of peptides representing various regions of the bindin sequence to inhibit fertilization. Twenty-four peptides were studied: 7 based on the Strongylocentrotus purpuratus bindin sequence, 11 based on the S. franciscanus bindin sequence, and 6 control peptides. Values for the concentration of peptide required to inhibit 50% of the productive sperm contacts (IC50) were extracted from experimental measurements of the extent of fertilization in the presence of various concentrations. of these peptides. The IC50 value averaged 220 microM for the control peptides. Active peptides representing certain specific subregions of the bindin sequence displayed IC50 values < 10% of the average value for control peptides, and the IC50 for the most potent of the peptides tested was only approximately 1% of the control peptide value (IC50 = 2.2 microM). Furthermore, we found that a peptide representing a particular region of the S. franciscanus bindin sequence that differs from the S. purpuratus bindin sequence inhibits fertilization species specifically. For the reaction of S. purpuratus sperm and eggs, the IC50 of this peptide was approximately 120 microM, whereas for the reaction of S. franciscanus sperm and eggs it was only 8.6 microM. These results demonstrate that a few specific regions of the bindin molecule are involved in the sperm-egg contact and that certain of these regions mediate the species specificity of the interaction in a sequence- specific manner.", "pmcid": "PMC300939", "issn": "1059-1524", "publisher": "American Society for Cell Biology", "publication": "Molecular Biology of the Cell", "publication_date": "1993-04", "series_number": "4", "volume": "4", "issue": "4", "pages": "375-387" }, { "id": "authors:9tas8-3dn43", "collection": "authors", "collection_id": "9tas8-3dn43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160331-082533600", "type": "article", "title": "Forbidden Synonymous Substitutions in Coding Regions", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "In the evolution of highly conserved genes, a few \"synonymous\" substitutions at third bases that would not alter the protein sequence are forbidden or very rare, presumably as a result of functional requirements of the gene or the messenger RNA. Another 10% or 20% of codons are significantly less variable by synonymous substitution than are the majority of codons. The changes that occur at the majority of third bases are subject to codon usage restrictions. These usage restrictions control sequence similarities between very distant genes. For example, 70% of third bases are identical in calmodulin genes of man and trypanosome. Third-base similarities of distant genes for conserved proteins are mathematically predicted, on the basis of the G+C composition of third bases. These observations indicate the need for reexamination of methods used to calculate synonymous substitutions.", "issn": "0737-4038", "publisher": "Oxford University Press", "publication": "Molecular Biology and Evolution", "publication_date": "1993-01", "series_number": "1", "volume": "10", "issue": "1", "pages": "205-220" }, { "id": "authors:623tf-yyz94", "collection": "authors", "collection_id": "623tf-yyz94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160308-070622092", "type": "book_section", "title": "DNA-DNA hybridization of single-copy DNA sequences", "book_title": "Molecular Evolution: Producing the Biochemical Data", "author": [ { "family_name": "Springer", "given_name": "Mark S.", "clpid": "Springer-M-S" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "contributor": [ { "family_name": "Zimmer", "given_name": "Elizabeth A.", "clpid": "Zimmer-E-A" } ], "abstract": "This chapter is reviews the basic principles of hybridization and the kinetics of reassociation. It provides an overview that summarizes and compares different techniques used in single-copy hybridization. The chapter then examines different estimates of distance derived from melting curves. Native DNA is isolated and purified to remove RNA and protein. Long-stranded DNA is then sheared to short fragments to permit the separation of repetitive and single-copy DNA and to reduce viscosity and gel formation. The chapter also explains the kinetics of reassociation. Rates of reassociation of DNA are influenced by several factors including genome complexity, DNA concentration, fragment size, reassociation temperature, and cation concentration. The complexity of the sheared genome is the length in base pairs (bp) of the longest nonrepeating sequence that is produced by splicing together fragments in the population. The rate of reassociation is inversely proportional to the complexity of the genome. The hybridization of tracer DNA with driver DNA is also overviewed in the chapter.", "doi": "10.1016/0076-6879(93)24018-P", "isbn": "9780121821258", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "1993", "pages": "232-243" }, { "id": "authors:fxrvk-vcx68", "collection": "authors", "collection_id": "fxrvk-vcx68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160401-113735010", "type": "article", "title": "Phylogenetic Relationships of Reverse Transcriptase and RNase H Sequences and Aspects of Genome Structure in the Gypsy Group of Retrotransposons", "author": [ { "family_name": "Springer", "given_name": "Mark S.", "clpid": "Springer-M-S" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The gypsy group of long-terminal-repeat retrotransposons contains elements having the same order of enzyme domains in the pol gene as do retroviruses. Elements in the gypsy group are now known from yeast, filamentous fungi, plants, insects, and echinoids. Reverse transcriptase and RNase H amino acid sequences from elements in the gypsy group--including the recently described SURL elements, TED, Cft1, and Ulysses,--were aligned and analyzed by using parsimony and bootstrapping methods, with plant caulimoviruses and/or retroviruses as outgroups. Clades supported at the 95% level after bootstrapping include (1) 17.6 with 297 and (2) all of the SURL elements together. Other likely relationships supported at lower bootstrap confidence intervals include (1) SURL elements with mag, (2) 17.6 and 297 with TED, and this collective group with 412 and gypsy, (3) Tf1 with Cft1, (4) IFG7 with Del, and (5) all of the retrotransposons in the gypsy group together, to the exclusion of Ty3. In contrast with an earlier analysis, our results place mag within the gypsy group rather than outside of a cluster that contains gypsy group retrotransposons and plant caulimoviruses. Several features of retrotransposon genomes provide further support for some of the aforementioned relationships. The union of SURL elements with mag is supported by the presence of two RNA binding sites in the nucleocapsid protein. Location of the tRNA primer binding site and the presence of a long open reading frame 3' to the pol gene support the 17.6-297-TED-412-gypsy cluster.", "issn": "0737-4038", "publisher": "Oxford University Press", "publication": "Molecular Biology and Evolution", "publication_date": "1993", "series_number": "6", "volume": "10", "issue": "6", "pages": "1370-1379" }, { "id": "authors:weakt-xhr79", "collection": "authors", "collection_id": "weakt-xhr79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HARpnas92", "type": "article", "title": "Complexity of Sea Urchin Embryo Nuclear Proteins That Contain Basic Domains", "author": [ { "family_name": "Harrington", "given_name": "Michael G.", "orcid": "0000-0002-7923-8032", "clpid": "Harrington-M-G" }, { "family_name": "Coffman", "given_name": "James A.", "clpid": "Coffman-J-A" }, { "family_name": "Calzone", "given_name": "Frank J.", "clpid": "Calzone-F-J" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "We describe a quantitative two-dimensional gel electrophoretic analysis of nuclear extract from 24-hr sea urchin embryos. The extract was fractionated by using a weak cation-exchange resin, and eight known DNA-binding proteins were shown to be entirely included in a salt eluate that releases proteins containing basic domains. This fraction and a lower-salt fraction containing the majority of the protein species were mapped two-dimensionally by using new algorithms that permit reproducible spot identification, storage of intensity and map-position data, and subtractive comparison of one pattern with respect to another. By reference to a previously characterized DNA-binding factor, spot intensity could be interpreted in terms of the number of molecules per embryo nucleus. A map was constructed displaying all nuclear proteins containing basic domains that are present within the concentration range per nucleus of a set of known DNA-binding factors of the sea urchin embryo. The map includes 265 spots that fulfill both of these criteria, probably representing about 100 different protein species.", "pmcid": "PMC49478", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1992-07-15", "series_number": "14", "volume": "89", "issue": "14", "pages": "6252-6256" }, { "id": "authors:s34ph-frr52", "collection": "authors", "collection_id": "s34ph-frr52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121023-152628630", "type": "article", "title": "Territorial Expression of Three Different trans-Genes in Early Sea Urchin Embryos Detected by a Whole-Mount Fluorescence Procedure", "author": [ { "family_name": "Zeller", "given_name": "Robert W.", "clpid": "Zeller-R-W" }, { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Franks", "given_name": "Roberta R.", "clpid": "Franks-R-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "We have developed a new procedure for detection of the protein product of chloramphenicol acetyltransferase (CAT) reporter genes in whole mounted sea urchin embryos. The position of a commercially available anti-CAT antibody is visualized by video or confocal microscopy, and thus the spatial domains of exogenous reporter gene expression can be determined with regard to the intact three-dimensional structures of the embryo. We show that in pluteus stage embryos CAT protein expression patterns for SM50\u00b7CAT or CyIII\u0251\u00b7CAT reporter genes are similar to those previously obtained by in situ hybridizations with radioactive probes. Taking advantage of the superior resolution of cellular CAT expression patterns using the antibody visualization method, we found for the first time that, in addition to the expression in aboral ectoderm, some cells in the ciliated band of the pluteus express CyIII\u0251\u00b7CAT. The expression of a new fusion construct, CyII\u0251\u00b7CAT, was also examined. As expected from the localization of endogenous CyII\u0251 mRNA, CAT protein was expressed under control of the CyII\u0251 promoter in gut and skeletogenic mesenchyme cells.", "doi": "10.1016/0012-1606(92)90178-J", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1992-06", "series_number": "2", "volume": "151", "issue": "2", "pages": "382-390" }, { "id": "authors:ne8sv-kng72", "collection": "authors", "collection_id": "ne8sv-kng72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas92", "type": "article", "title": "Graviton scattering and matter distribution", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "In this model gravitation results from the emission and absorption of quanta (gravitons) that are scattered a few times in crossing a typical galaxy. Many features of the universe can be explained in terms of this model, although theoretical justification for the scattering of gravitons is lacking. Gravitons follow a random walk and diffuse through the outer regions of a galaxy. As a result the force of attraction follows a 1/R law, matching observed galactic rotation curves and explaining galactic dynamics without the need of dark matter. The model makes predictions regarding early stages in the expansion of the universe and the establishment of the mass distribution. It may be assumed that a nearly uniform expanding cloud of gas was present that was subject to collapse under gravitational forces. The 1/R law of attraction due to graviton diffusion is orders of magnitude more effective for initiation of collapse than the inverse square law, and it applies to blocks of gas larger than the graviton mean free path. Delay in the spread of gravitational attraction by diffusion sets a time-dependent range beyond which the attractive force is zero. In the model this causes arrays of matter to collapse locally into zones with a spacing set by the length of the range of the attractive force. An initial examination indicates that under these conditions the background radiation could have been released from a nearly uniform distribution at the time of decoupling of radiation and matter, followed by gravitational collapse into blocks of galactic mass. In the model the diffusion of gravitons continued and collapse became possible on a larger scale, initiating the formation of galactic clusters and still larger structures. The slow rate of diffusion then prevented the largest structures from attracting each other and permitted the formation of the voids on a very large scale. The model predicts that on the largest scale there is a three-dimensional repeated array of structures separated by voids. Ultimately structures larger than galactic clusters outran the diffusion of the gravitons and have since been freely expanding.", "pmcid": "PMC525637", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1992-05-01", "series_number": "9", "volume": "89", "issue": "9", "pages": "4086-4090" }, { "id": "authors:k1yax-f3250", "collection": "authors", "collection_id": "k1yax-f3250", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151218-081157341", "type": "article", "title": "Calculation of sequence divergence from the thermal stability of DNA heteroduplexes", "author": [ { "family_name": "Springer", "given_name": "Mark S.", "clpid": "Springer-M-S" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Measurements are reported of the thermal stability of DNA heteroduplexes between clones of the eta-globin pseudogene from a variety of primates. The known sequences of this 7.1-kb region differ from each over a range from 1.6% for human versus chimp to nearly 12% for human versus spider monkey. Thermal stability was determined by standard hydroxyapatite thermal elution, and the results show a precisely linear decrease in thermal stability with divergence. The slope of the regression line is 1.18% sequence divergence per degree centigrade reduction in thermal stability.", "doi": "10.1007/BF00162994", "issn": "0022-2844", "publisher": "Springer Verlag", "publication": "Journal of Molecular Evolution", "publication_date": "1992-05", "series_number": "5", "volume": "34", "issue": "5", "pages": "379-382" }, { "id": "authors:p5ckp-enx77", "collection": "authors", "collection_id": "p5ckp-enx77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151218-080949915", "type": "article", "title": "Automated sequential affinity chromatography of sea urchin embryo DNA binding proteins", "author": [ { "family_name": "Coffman", "given_name": "J. A.", "clpid": "Coffman-J-A" }, { "family_name": "Moore", "given_name": "J. G.", "clpid": "Moore-J-G" }, { "family_name": "Calzone", "given_name": "F. J.", "clpid": "Calzone-F-J" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Hood", "given_name": "L. E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" } ], "abstract": "An automated method of running a tandem sequence of oligonucleotide affinity columns was used to purify factors that interact specifically with cis-regulatory sites of the CyIIIa cytoskeletal actin gene of the sea urchin embryo (Strongylocentrotus purpuratus). The method allows quantitative enrichment in a single chromatographic run of up to 12 different sequence-specific DNA binding proteins, each of which may then be readily purified to homogeneity by methods such as preparative gel electrophoresis. The affinity chromatography and identification of six different CyIIIa-regulatory factors is described, and the general utility of the method is discussed.", "issn": "1053-6426", "publisher": "Springer", "publication": "Molecular Marine Biology and Biotechnology", "publication_date": "1992-04", "series_number": "2", "volume": "1", "issue": "2", "pages": "136-46" }, { "id": "authors:gz9mz-cvc76", "collection": "authors", "collection_id": "gz9mz-cvc76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SMImbc92", "type": "article", "title": "SpCoel1: a sea urchin profilin gene expressed specifically in coelomocytes in response to injury", "author": [ { "family_name": "Smith", "given_name": "L. Courtney", "clpid": "Smith-L-C" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "SpCoel1 is a single copy gene that is specifically expressed in most of the coelomocytes of the adult purple sea urchin, Strongylocentrotus purpuratus. The 4-kb transcript from this gene has a relatively short (426 nucleotide) open reading frame (ORF) with long 3' and 5' untranslated regions. The ORF encodes a protein that has strong amino acid sequence similarity to profilins from yeast to mammals. Transcript titrations of SpCoel1 show significant increases per coelomocyte in animals that have been physiologically challenged. Increases in transcript levels are of similar magnitudes between animals receiving different treatments, such as injuries from needle punctures or from injections of foreign cells. The evidence presented here implies a molecular mechanism by which this lower deuterostome defense system responds to external insult, viz that an external \"injury signal\" activates a signal transduction system, which in turn mediates the alterations in cytoskeletal state that are required for coelomocyte activation.", "pmcid": "PMC275591", "issn": "1059-1524", "publisher": "American Society for Cell Biology", "publication": "Molecular Biology of the Cell", "publication_date": "1992-04", "series_number": "4", "volume": "3", "issue": "4", "pages": "403-414" }, { "id": "authors:ev4ft-8b864", "collection": "authors", "collection_id": "ev4ft-8b864", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120417-132121074", "type": "article", "title": "Macromere cell fates during sea urchin development", "author": [ { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "This paper examines the cell lineage relationships and cell fates in embryos of the sea urchin Strongylocentrotus purpuratus leading to the various cell types derived from the definitive vegetal plate territory or the veg_2 tier of cells. These cell types are gut, pigment cells, basal cells and coelomic pouches. They are cell types that constitute embryonic structures through cellular migration or rearrangement unlike the relatively non-motile ectoderm cell types. For this analysis, we use previous knowledge of lineage to assign macromeres to one of four types: VOM, the oral macromere; VAM, the aboral macromere, right and left VLM, the lateral macromeres. Each of the four macromeres contributes progeny to all of the cell types that descend from the definitive vegetal plate. Thus in the gut each macromere contributes to the esophagus, stomach and intestine, and the stripe of labeled cells descendant from a macromere reflects the re-arrangement of cells that occurs during archenteron elongation. Pigment cell contributions exhibit no consistent pattern among the four macromeres, and are haphazardly distributed throughout the ectoderm. Gut and pigment cell contributions are thus radially symmetrical. In contrast, the VOM blastomere contributes to both of the coelomic pouches while the other three macromeres contribute to only one or the other pouch. The total of the macromere contribution amounts to 60% of the cells constituting the coelomic pouches.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1991-12", "series_number": "4", "volume": "113", "issue": "4", "pages": "1085-1091" }, { "id": "authors:8sc36-1ny35", "collection": "authors", "collection_id": "8sc36-1ny35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160331-111921056", "type": "article", "title": "Comparison of the Hindin Proteins of Strongylocentrotus franciscanus, S. purpuratus, and Lytechinus variegatus: Sequences involved in the Species Specificity of Fertilization", "author": [ { "family_name": "Minor", "given_name": "Joseph E.", "clpid": "Minor-J-E" }, { "family_name": "Fromson", "given_name": "David R.", "clpid": "Fromson-D-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Bindin is the sea urchin sperm acrosomal protein that is responsible for the species-specific adhesion of the sperm to the egg. Two new bindin cDNA sequences that contain the entire open reading frame for the binding precursor are reported: one for Strongylocentrotus franciscanus and one for Lytechinus variegatus. Both contain inverted repetitive sequences in their 3' untranslated regions, and the S. franciscanus cDNA contains an inverted repetitive sequence match between the 5' untranslated region and the coding region. The middle third of the mature bindin sequence is highly conserved in all three species, and the flanking sequences share short repeated sequences that vary in number between the species. Cross-fertilization data are reported for the species S. purpuratus, S. franciscanus, L. variegatus, and L. pictus. A barrier to cross-fertilization exists between the sympatric Strongylocentrotus species, but there is no barrier between the allopatric Lytechinus species.", "issn": "0737-4038", "publisher": "Oxford University Press", "publication": "Molecular Biology and Evolution", "publication_date": "1991-11-01", "series_number": "6", "volume": "8", "issue": "6", "pages": "781-795" }, { "id": "authors:f7vn9-14f64", "collection": "authors", "collection_id": "f7vn9-14f64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SPRIpnas91", "type": "article", "title": "Retroviral-Like Element in a Marine Invertebrate", "author": [ { "family_name": "Springer", "given_name": "Mark S.", "clpid": "Springer-M-S" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Retroviral-like elements (RL elements) include retroviruses and long terminal repeat (LTR)-containing retrotransposons. We report the presence of sea urchin RL elements (termed SURL) in eight species of sea urchins and find that these RL elements belong to several subfamilies. The complete DNA sequence of one SURL element in Tripneustes gratilla is 5266 base pairs long, including 254-nucleotide-long identical long terminal repeats (LTRs). It contains a single open reading frame nearly 4 kilobases long including the gag and pol genes. Comparison of conserved DNA sequences of RL elements from different sea urchin species indicates that active elements have been inserting copies into echinoid genomes for at least 200 million years.", "pmcid": "PMC52516", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1991-10-01", "series_number": "19", "volume": "88", "issue": "19", "pages": "8401-8404" }, { "id": "authors:73s2a-mmz89", "collection": "authors", "collection_id": "73s2a-mmz89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:LIVdev91", "type": "article", "title": "Differential stability of expression of similarly specified endogenous and exogenous genes in the sea urchin embryo", "author": [ { "family_name": "Livant", "given_name": "Donna L.", "clpid": "Livant-D-L" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Moore", "given_name": "James G.", "clpid": "Moore-J-G" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The object of these experiments was to determine whether competitive titration in vivo of factors required for expression of the CyIIIa\u00b7CAT fusion gene would affect expression of the endogenous CyIIIa gene in the same embryos. Earlier work showed that expression of this fusion gene after injection into sea urchin eggs is stoichiometrically reduced when low molar excesses of DNA fragments containing only its regulatory domain are coinjected. In order to compare endogenous (i.e. CyIIIa) and exogenous (i.e. CyIIIa\u00b7CAT) expression simultaneously in embryos bearing excess competitor regulatory DNA, we developed, and here describe, a new procedure for generating transgenic sea urchin embryos in which all of the cells in many embryos, and most in others, bear the exogenous DNA. Such large reduction of mosaicism can be achieved by multiple injection of the exogenous DNA fragments into fertilized eggs. Using this method, we demonstrate that at a level of competitor DNA incorporation which reduces CyIIIa\u00b7CAT expression by 85%, endogenous CyIIIa mRNA levels are wholly unaffected. Nor is spatial expression of the endogenous CyIIIa gene disturbed. Since the CyIIIa\u00b7CAT genes are properly expressed under control of the CyIIIa regulatory sequences, they must participate in the same set of necessary DNA-protein interactions. However, we infer from the results that we report here that the regulatory complexes in the endogenous CyIIIa gene are greatly stabilized relative to those of the exogenous CyIIIa\u00b7CAT genes.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1991-10", "series_number": "2", "volume": "113", "issue": "2", "pages": "385-398" }, { "id": "authors:bt3b4-fk847", "collection": "authors", "collection_id": "bt3b4-fk847", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120329-110241098", "type": "article", "title": "Gene regulatory factors of the sea urchin embryo. I. Purification by affinity chromatography and cloning of P3A2, a novel DNA-binding protein", "author": [ { "family_name": "Calzone", "given_name": "Frank J.", "clpid": "Calzone-F-J" }, { "family_name": "H\u00f6\u00f6g", "given_name": "Christer", "clpid": "H\u00f6\u00f6g-C" }, { "family_name": "Teplow", "given_name": "David B.", "clpid": "Teplow-D-B" }, { "family_name": "Cutting", "given_name": "Ann E.", "orcid": "0000-0001-9721-4811", "clpid": "Cutting-A-E" }, { "family_name": "Zeller", "given_name": "Robert W.", "clpid": "Zeller-R-W" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The P3A2 regulatory protein interacts with specific sites in the control region of the CyIIIa actin gene. Previous studies showed that this interaction is required to confine expression of a CyIIIa.CAT fusion to the aboral ectoderm, the embryonic territory in which CyIIIa is normally utilized. P3A2 also binds specifically to similar target sites located in the regulatory region of the SM50 gene, which is expressed only in skeletogenic mesenchyme lineages. The P3A2 factor was purified by affinity chromatography from nuclear extracts of 24 h sea urchin embryos, and partial peptide sequences were used to isolate a cDNA clone encoding the complete protein. There are no significant similarities between P3A2 and any other protein in existing sequence data bases. P3A2 thus includes a novel type of DNA-binding domain. To examine the differential utilization of P3A2 in CyIIIa and SM50 genes, we measured the specific affinity of this protein for the various target sites in the regulatory DNAs of each gene, and identified the core target site sequences. The stability of P3A2 complexes formed with SM50 target sites is 50\u2013100 times greater than that of the complexes formed with CyIIIa target sites, though the factor binds to very similar core sequence elements. P3A2 is one of at least twelve different proteins whose interaction with CyIIIa regulatory DNA is required for correct developmental expression. The results reported demonstrate that it might be possible to purify most of these regulatory proteins, or any other specific DNA-binding proteins of the sea urchin embryo, by using the simple procedures described for P3A2.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1991-05", "series_number": "1", "volume": "112", "issue": "1", "pages": "335-350" }, { "id": "authors:bemwv-xxx49", "collection": "authors", "collection_id": "bemwv-xxx49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HOOdev91", "type": "article", "title": "Gene regulatory factors of the sea urchin embryo. II. Two dissimilar proteins, P3A1 and P3A2, bind to the same target sites that are required for early territorial gene expression", "author": [ { "family_name": "H\u00f6\u00f6g", "given_name": "Christer", "clpid": "H\u00f6\u00f6g-C" }, { "family_name": "Calzone", "given_name": "Frank J.", "clpid": "Calzone-F-J" }, { "family_name": "Cutting", "given_name": "Ann E.", "orcid": "0000-0001-9721-4811", "clpid": "Cutting-A-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Previous work demonstrated that a negative regulatory interaction mediated by factor(s) termed 'P3A' is required for correct territory-specific gene expression in the sea urchin embryo. A probe derived from a P3A target site in the skeletogenic SM50 gene of Strongylocentrotus purpuratus was used to isolate a cDNA clone coding for a factor that binds specifically to this site. This factor, called P3A1, contains two sequence elements that belong to the Zn finger class of DNA-binding motifs, and in these regions is most closely similar to the Drosophila hunchback factor. The P3A1 factor also binds to a similar target sequence in a second gene, CyIIIa, expressed in embryonic aboral ectoderm. Another sea urchin embryo protein factor, P3A2, has been isolated by affinity chromatography and cloned, as described in Calzone et al. Development 112, 335-350 (1991). P3A2 footprints the same target sites in the SM50 and CyIIIa genes as does P3A1, but lacks the Zn finger sequence motifs and in amino acid sequence is almost entirely dissimilar to P3A1. A deletion analysis of P3A2 delimited the DNA-binding region, revealing that five specific amino acids in the first P3A1 finger region and four in the second P3A1 finger region are also present in equivalent positions in P3A2. The P3A1 and P3A2 factors could function as regulatory antagonists, having evolved similar target specificities from dissimilar DNA-binding domains.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1991-05", "series_number": "1", "volume": "112", "issue": "1", "pages": "351-364" }, { "id": "authors:s6dg8-xws74", "collection": "authors", "collection_id": "s6dg8-xws74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121023-145952434", "type": "article", "title": "Locale and Level of Bindin mRNA in Maturing Testis of the Sea Urchin, Strongylocentrotus purpuratus", "author": [ { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Minor", "given_name": "Joseph E.", "clpid": "Minor-J-E" }, { "family_name": "Nishioka", "given_name": "David", "clpid": "Nishioka-David" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "This first study of the onset of spermatogenesis in the sea urchin, Strongylocentrotus purpuratus, was undertaken using individuals reared in the laboratory. Spermatogenesis commences about 11\u201312 months after metamorphosis in these animals. Bindin message accumulates in late spermatocytes and early spermatids which lie in the luminal germinal layer. Bindin message accumulates later than does the testis-specific histone, H2b-1, suggesting that different classes of genes are sequentially activated during the differentiation of sperm. We correlate the number of bindin mRNA molecules with morphological structure and with quantitative aspects of gonad maturation including the number of nuclei and of sperm. The results suggest that the bindin mRNA concentration in total RNA from testis at different stages of maturation reflects the change in the proportion of expressing cells in the total cell population of the testis.", "doi": "10.1016/0012-1606(90)90149-D", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1990-11", "series_number": "1", "volume": "142", "issue": "1", "pages": "44-49" }, { "id": "authors:386dz-ccf68", "collection": "authors", "collection_id": "386dz-ccf68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CUTpnas90", "type": "article", "title": "Rare maternal mRNAs code for regulatory proteins that control lineage-specific gene expression in the sea urchin embryo", "author": [ { "family_name": "Cutting", "given_name": "Ann E.", "orcid": "0000-0001-9721-4811", "clpid": "Cutting-A-E" }, { "family_name": "H\u00f6\u00f6g", "given_name": "Christer", "clpid": "H\u00f6\u00f6g-C" }, { "family_name": "Calzone", "given_name": "Frank J.", "clpid": "Calzone-F-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The prevalence of mRNAs coding for the sea urchin embryo regulatory factors P3A1 and P3A2 was measured by single-strand probe excess solution hybridization. P3A1 and P3A2 are not homologous proteins, though they both bind specifically to a particular cis-regulatory sequence. Interaction at this target site is known to be required for lineage-specific expression of an aboral ectoderm-specific gene and probably for several other genes as well. Genome blot hybridizations show that both factors are encoded by single-copy genes. Maternal mRNAs for both factors are present at less than 10^3 molecules per egg, which places them in the rare mRNA class. During development to the mesenchyme blastula stage, the amount of P3A1 mRNA (per embryo) increases severalfold while that of P3A2 remains approximately constant. Specification of the aboral ectoderm founder cells and of their initial patterns of gene expression must occur during early to mid-cleavage stage. Therefore, the regulatory proteins needed for this process must be produced by this stage. We show that the quantities of the P3A proteins that can be synthesized from the numbers of mRNA molecules present in the large blastomeres of the early embryo are sufficient to be functional, because these proteins will be accumulated in the nuclei. Thus maternal P3A1 or P3A2 proteins are not required, nor were these detected in earlier studies. Furthermore, differential spatial (as well as temporal) distribution of both of these newly synthesized factor species could result from the unequal cleavage pattern utilized in the sea urchin egg.", "pmcid": "PMC54870", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1990-10-15", "series_number": "20", "volume": "87", "issue": "20", "pages": "7953-7957" }, { "id": "authors:1fz91-7h517", "collection": "authors", "collection_id": "1fz91-7h517", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HOUdev90", "type": "article", "title": "Negative spatial regulation of the lineage specific CyIIIa actin gene in the sea urchin embryo", "author": [ { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Franks", "given_name": "Roberta R.", "clpid": "Franks-R-R" }, { "family_name": "Zeller", "given_name": "Robert W.", "clpid": "Zeller-R-W" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The CyIIIa\u00b7CAT fusion gene was injected into Strongylocentrotus purpuratus eggs, together with excess ligated competitor sequences representing subregions of the CyIIIa regulatory domain. In this construct, the chloramphenicol acetyltransferase (CAT) reporter gene is placed under the control of the 2300 nucleotide upstream regulatory domain of the lineage-specific CyIIIa cytoskeletal actin gene. CAT mRNA was detected by in situ hybridization in serial sections of pluteus stage embryos derived from the injected eggs. When carrier DNA lacking competitor CyIIIa fragments was coinjected with CyIIIa.CAT, CAT mRNA was observed exclusively in aboral ectoderm cells, i.e. the territory in which the CyIIIa gene itself is normally expressed (as also reported by us previously). The same result was obtained when five of seven different competitor subfragments bearing sites of DNA-protein interaction were coinjected. However, coinjection of excess quantities of either of two widely separated, nonhomologous fragments of the CyIIIa regulatory domain produced a dramatic ectopic expression of CAT mRNA in the recipient embryos. CAT mRNA was observed in gut, mesenchyme cells and oral ectoderm in these embryos. We conclude that these fragments contain regulatory sites that negatively control spatial expression of the CyIIIa gene.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1990-09", "series_number": "1", "volume": "110", "issue": "1", "pages": "41-50" }, { "id": "authors:ng7qh-ms612", "collection": "authors", "collection_id": "ng7qh-ms612", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:FRAdev90", "type": "article", "title": "Competitive titration in living sea urchin embryos of regulatory factors required for expression of the CyIIIa actin gene", "author": [ { "family_name": "Franks", "given_name": "Roberta R.", "clpid": "Franks-R-R" }, { "family_name": "Anderson", "given_name": "Roger", "clpid": "Anderson-R" }, { "family_name": "Moore", "given_name": "James G.", "clpid": "Moore-J-G" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Previous studies have located some twenty distinct sites within the 2.3 kb 5' regulatory domain of the sea urchin CyIIIa cytoskeletal actin gene, where there occur in vitro high-specificity interactions with nuclear DNA-binding proteins of the embryo. This gene is activated in late cleavage, exclusively in cells of the aboral ectoderm cell lineages. In this study, we investigate the functional importance in vivo of these sites of DNA-protein interaction. Sea urchin eggs were coinjected with a fusion gene construct in which the bacterial chloramphenicol acetyltransferase (CAT) reporter gene is under the control of the entire CyIIIa regulatory domain, together with molar excesses of one of ten nonoverlapping competitor subfragments of this domain, each of which contains one or a few specific site(s) of interaction. The exogenous excess binding sites competitively titrate the available regulatory factors away from the respective sites associated with the CyIIIa.CAT reporter gene. This provides a method for detecting in vivo sites within the regulatory domain that are required for normal levels of expression, without disturbing the structure of the regulatory domain. We thus identify five nonoverlapping regions of the regulatory DNA that apparently function as binding sites for positively acting transcriptional regulatory factors. Competition with a subfragment bearing an octamer site results in embryonic lethality. We find that three other sites display no quantitative competitive interference with CyIIIa.CAT expression, though as shown in the accompanying paper, two of these sites are required for control of spatial expression. We conclude that the complex CyIIIa regulatory domain must assess the state of many distinct and individually necessary interactions in order to properly regulate CyIIIa transcriptional activity in development.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1990-09", "series_number": "1", "volume": "110", "issue": "1", "pages": "31-40" }, { "id": "authors:2rhxw-7q097", "collection": "authors", "collection_id": "2rhxw-7q097", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151218-080936398", "type": "article", "title": "Rapid evolution in a fraction of the Drosophila nuclear genome", "author": [ { "family_name": "Werman", "given_name": "Steven D.", "clpid": "Werman-S-D" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Previous observations have indicated thatDrosophila DNA contains a component that evolves so rapidly that it fails to hybridize between the DNAs of sibling species. To establish the reality of this component and study its properties, the fraction (about 20%) of Drosophila simulans (Dsim) DNA that fails to hybridize to Drosophila melanogaster (Dmel) DNA has been isolated. The majority of the hybridizable part of this isolated fraction (based on control tests on Dsim DNA) fails to hybridize with Dmel DNA under the conditions used for the initial fractionation. Clones of this fraction do hybridize with Dmel DNA at open criterion producing duplexes with greatly reduced thermal stability, indicating that the underlying process is rapid sequence divergence rather than loss of the homologous sequences by relatively large deletions. \n\nCloned fragments from the nonhybridizing fraction from Dsim are more than 15% divergent from the Dmel homologues, whereas the fraction that does hybridize is only 3\u20135% divergent. In comparison, synonymous substitutions in the coding regions of five genes show a 9% average divergence between Dsim and Dmel. They appear to be intermediate in their degree of divergence between the hybridizing and nonhybridizing components.", "doi": "10.1007/BF02099998", "issn": "0022-2844", "publisher": "Springer Verlag", "publication": "Journal of Molecular Evolution", "publication_date": "1990-03", "series_number": "3", "volume": "30", "issue": "3", "pages": "281-289" }, { "id": "authors:mx77z-nfs89", "collection": "authors", "collection_id": "mx77z-nfs89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151224-073924482", "type": "article", "title": "Comment on DNA hybridization issues raised at Lake Arrowhead", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "[no abstract]", "doi": "10.1007/BF02099990", "issn": "0022-2844", "publisher": "Springer Verlag", "publication": "Journal of Molecular Evolution", "publication_date": "1990-03", "series_number": "3", "volume": "30", "issue": "3", "pages": "193-195" }, { "id": "authors:9pa8p-1n829", "collection": "authors", "collection_id": "9pa8p-1n829", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151218-080936736", "type": "article", "title": "Sequences of the CyIIIa actin gene regulatory domain bound specifically by sea urchin embryo nuclear proteins", "author": [ { "family_name": "Th\u00e9z\u00e9", "given_name": "Nadine", "clpid": "Th\u00e9z\u00e9-N" }, { "family_name": "Calzone", "given_name": "Frank J.", "clpid": "Calzone-F-J" }, { "family_name": "Thiebaud", "given_name": "Pierre", "clpid": "Thiebaud-P" }, { "family_name": "Hill", "given_name": "Ronald L.", "clpid": "Hill-R-L" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Expression of the Cylla cytoskeletal actin gene is a marker of differential gene activation in the aboral ectoderm of the early sea urchin embryo. Gene transfer expreiments have defined a 2,300 nucleotide cis-regulatory domain required for the correct spatial and temporal control of this gene. This domain includes at least 20 sites at which relatively stable DNA-protein complexes form in vitro on reaction with embryo nuclear extracts. We report the nucleotide sequence of the whole regulatory domain and map the sites at which high-specificity DNA-protein interactions occur. These were located initially by gel shift assays carried out on progressive restriction digests of given subfragments of the large regulatory domain and were located more exactly by oligonucleotide gel shift competitions. Eight of the sites of specific interaction are unique within the Cyllla regulatory domain, and the remainder consist of five different sites that occur more than once. We observe some well known sequences also found in regulatory regions of other genes, e.g., \"CCAAT\" and \"octamer\" elements. The various sites have been classified regarding putative biological function in other work, and the present studies permit an assessment of the number and complexity of interactions constituting each functional class and of the relative locations of sites of each class.", "doi": "10.1002/mrd.1080250203", "issn": "1040-452X", "publisher": "Wiley-Liss", "publication": "Molecular Reproduction and Development", "publication_date": "1990-02", "series_number": "2", "volume": "25", "issue": "2", "pages": "110-122" }, { "id": "authors:8j5dr-vf260", "collection": "authors", "collection_id": "8j5dr-vf260", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121023-112006174", "type": "article", "title": "Segregation of Oral from Aboral Ectoderm Precursors Is Completed at Fifth Cleavage in the Embryogenesis of Strongylocentrotus purpuratus", "author": [ { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A specific set of founder cells uniquely gives rise to the oral and aboral ectoderms in the regularly developing sea urchin Strongylocentrotus purpuratus. We showed earlier that the polar No and Na (animal oral and animal aboral) blastomeres are specified by third cleavage, while the respective oral and aboral lineage contributions of the left and right NL (animal lateral) blastomeres have not yet segregated from one another at third cleavage. Here we demonstrate by iontophoretic injection of lysyl rhodamine dextran lineage tracer that segregation of oral vs aboral cell fates in the lineages of the NL blastomeres has still not occurred by fourth cleavage, but at fifth cleavage there arise from the NL sublineages founder cells whose progeny contribute exclusively to the aboral ectoderm. The sister cells of these fifth cleavage blastomeres are founder cells that contribute exclusively to oral structures. The aboral ectoderm tracts to which NL derivatives give rise occupy lateral regions of the anterior aboral ectoderm, while the oral structures deriving from the NL blastomeres are the lateral sectors of the ciliated bands. The cells of the ciliated bands do not express aboral ectoderm markers and are considered to constitute the border of the oral region. With these new findings we complete our knowledge of the origins, identities, and fates of the 11 founder cells, the progeny of which exclusively give rise to the aboral ectoderm, and of the 5 founder cells, the progeny of which exclusively produce the oral ectoderm and its derivatives.", "doi": "10.1016/0012-1606(90)90009-8", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1990-01", "series_number": "1", "volume": "137", "issue": "1", "pages": "77-85" }, { "id": "authors:mfshv-48z36", "collection": "authors", "collection_id": "mfshv-48z36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160401-142756314", "type": "article", "title": "Intersecting batteries of differentially expressed genes in the early sea urchin embryo", "author": [ { "family_name": "Thiebaud", "given_name": "Pierre", "clpid": "Thiebaud-P" }, { "family_name": "Goodstein", "given_name": "Marcia", "clpid": "Goodstein-M" }, { "family_name": "Calzone", "given_name": "Frank J.", "clpid": "Calzone-F-J" }, { "family_name": "Th\u00e9z\u00e9", "given_name": "Nadine", "clpid": "Th\u00e9z\u00e9-N" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "We determined the distribution of cis-regulatory sites, previously identified in the control domain of the CyIIIa gene, in three other genes displaying diverse spatial patterns of expression in the sea urchin embryo. Competitive gel-shift reactions were carried out using probes from the CyIIIa gene, with competitor fragments isolated from the previously defined control domains of the other genes. CyIIIa is expressed only in aboral ectoderm lineages; the other genes studied were Spec1, also expressed in aboral ectoderm; CyI, expressed in many different cell types; and SM50, expressed only in skeletogenic mesenchyme. All four genes are activated at about the same time in late cleavage. Where competitive interactions indicated a functionally comparable binding site (in vitro), a sequence homology was sought, and in most cases could be identified. An interesting pattern of putative regulatory site usage emerges: Of 10 CyIIIa interactions tested, three only were unique to the CyIIIa gene with respect to the set of four genes tested; one believed on previous evidence to be a temporal regulator was shared by all four genes, and the remainder were shared in various subsets of the four genes.", "doi": "10.1101/gad.4.11.1999", "issn": "0890-9369", "publisher": "Cold Spring Harbor Laboratory Press", "publication": "Genes and Development", "publication_date": "1990", "series_number": "11", "volume": "4", "issue": "11", "pages": "1999-2010" }, { "id": "authors:e7sdr-vay20", "collection": "authors", "collection_id": "e7sdr-vay20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120510-091723549", "type": "article", "title": "The oral-aboral axis of a sea urchin embryo is specified by first cleavage", "author": [ { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Several lines of evidence suggest that the oral-aboral axis in Strongylocentrotus purpuratus embryos is specified at or before the 8-cell stage. Were the oral-aboral axis specified independently of the first cleavage plane, then a random association of this plane with the blastomeres of the four embryo quadrants in the oral-aboral plane (viz. oral, aboral, right and left) would be expected. Lineage tracer dye injection into one blastomere at the 2-cell stage and observation of the resultant labeling patterns demonstrates instead a strongly nonrandom association. In at least ninety percent of cases, the progeny of the aboral blastomeres are associated with those of the left lateral blastomeres and the progeny of the oral blastomeres with the right lateral ones, respectively. Thus, ninety percent of the time the oral pole of the future oral-aboral axis lies 45 degrees clockwise from the first cleavage plane as viewed from the animal pole. The nonrandom association of blastomeres after labeling of the 2-cell stage implies that there is a mechanistic relation between axis specification and the positioning of the first cleavage plane.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1989-08", "series_number": "4", "volume": "106", "issue": "4", "pages": "641-647" }, { "id": "authors:9gm58-q9q46", "collection": "authors", "collection_id": "9gm58-q9q46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas89", "type": "article", "title": "The current source of human Alu retroposons is a conserved gene shared with Old World monkey", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Stout", "given_name": "David B.", "clpid": "Stout-D-B" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A significant fraction of human Alu repeated sequences are members of the precise, recently inserted class. A cloned member of this class has been used as a probe for interspecies hybridization and thermal stability determination. The probe was reassociated with human, mandrill, and spider monkey DNA under conditions such that only almost perfectly matching duplexes could form. Equally precise hybrids were formed with human and mandrill DNA (Old World monkey) but not with spider monkey DNA (New World). These measurements as well as reassociation kinetics show the presence in mandrill DNA of many precise class Alu sequences that are very similar or identical in quantity and sequence to those in human DNA. Human and mandrill are moderately distant species with a single-copy DNA divergence of about 6%. Nevertheless, their recently inserted Alu sequences arise by retroposition of transcripts of source genes with nearly identical sequences. Apparently a gene present in our common ancestor at the time of branching was inherited and highly conserved in sequence in both the lineage of Old World monkeys and the lineage of apes and man.", "pmcid": "PMC287211", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1989-05-15", "series_number": "10", "volume": "86", "issue": "10", "pages": "3718-3722" }, { "id": "authors:6k9x3-2q039", "collection": "authors", "collection_id": "6k9x3-2q039", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151217-185657663", "type": "book_section", "title": "In vivo competition identifies positive cis-regulatory elements required for lineage-specific gene expression in the sea urchin embryo", "book_title": "Cellular Basis of Morphogenesis", "author": [ { "family_name": "Franks", "given_name": "Roberta R.", "clpid": "Franks-R-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "contributor": [ { "family_name": "Evered", "given_name": "David", "clpid": "Evered-D" }, { "family_name": "Marsh", "given_name": "Joan", "clpid": "Marsh-J" } ], "abstract": "Several cis-regulatory elements within the 5' regulatory region of the lineage-specific CyIIIa actin gene have been identified by in vivo competition. Sea urchin eggs were coinjected with a fusion construct in which the bacterial chloramphenicol acetyltransferase (CAT) gene is controlled by the CyIIIa regulatory domain, together with molar excesses of various DNA subfragments that are derived from this region. Each subfragment studied includes one or several known sites where highly specific interactions occur in vitro with nuclear DNA-binding proteins. Coinjection of excess molecules of some of these subregions results in a decrease in the activity of the CyIIIa-CAT fusion gene, as a function of the molar subfragment: CyIIIa-CAT ratio. This result implies that these sites complete with cis sequences linked to the CAT reporter gene for limited factors that positively regulate CyIIIa transcription in the embryo, and demonstrates the functional importance of a number of the DNA-protein interactions that have been observed in vitro.", "doi": "10.1002/9780470513798.ch9", "isbn": "9780471923060", "publisher": "Wiley", "place_of_publication": "Chichester, UK", "publication_date": "1989", "pages": "156-66; discussion 166" }, { "id": "authors:qzdq2-1v529", "collection": "authors", "collection_id": "qzdq2-1v529", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121023-104612076", "type": "article", "title": "Expression of two actin genes during larval development in the sea urchin Strongylocentrotus purpuratus", "author": [ { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "We report the first measurements of cell number, total RNA, and transcript accumulations for two actin genes during larval development of the sea urchin Strongylocentrotus purpuratus. At 5 weeks of feeding, when development of laboratory-raised larvae is completed, the cell number has increased about 100-fold with respect to the pluteus-stage embryo to about 150,000 \u00b1 50,000, and the total RNA has increased 46-fold to about 130 ng per larva. The transcripts of the Cylla cytoskeletal actin gene, which is expressed in adult tissues, continue to accumulate throughout larval development. A contrasting pattern of transcript accumulation is observed for Cyllla, a different cytoskeletal actin gene that in the embryo is expressed only in aboral ectoderm. These transcripts increase in number early in larval development, when the larval epidermis is differentiating, and then decline in quantity. It is known that at metamorphosis the larval epidermis is largely histolyzed and that the Cyllla gene is not expressed in the juvenile or adult.", "doi": "10.1002/mrd.1080010302", "issn": "1040-452X", "publisher": "Wiley-Blackwell", "publication": "Molecular Reproduction and Development", "publication_date": "1989", "series_number": "3", "volume": "1", "issue": "3", "pages": "149-155" }, { "id": "authors:04wwy-yah62", "collection": "authors", "collection_id": "04wwy-yah62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:LIVpnas88", "type": "article", "title": "An in vivo Titration of Regulatory Factors Required for Expression of a Fusion Gene in Transgenic Sea Urchin Embryos", "author": [ { "family_name": "Livant", "given_name": "Donna L.", "clpid": "Livant-D-L" }, { "family_name": "Cutting", "given_name": "Ann E.", "orcid": "0000-0001-9721-4811", "clpid": "Cutting-A-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "We report that endogenous regulatory factors mediating expression of a lineage-specific sea urchin embryo gene can be titrated in vivo by introduction of a sufficient molar excess of DNA-binding sites. Thus we obtain an estimate of the quantity of limiting factor(s) required for developmental activation and transcriptional expression, which can be compared with estimates of factor prevalence obtained by measurements in vivo carried out under equilibrium conditions. A fusion construct in which the bacterial gene for chloramphenicol acetyltransferase (CAT; acetyl-CoA:chloramphenicol O3-acetyltransferase, EC 2.3.1.28) is controlled by cis-regulatory elements of the CyIIIa cytoskeletal actin gene (CyIIIa-CAT) was introduced in varying numbers of copies into sea urchin eggs. The activity of the CyIIIa-CAT fusion gene in 24-hr blastula-stage embryos was shown to saturate as the number of exogenous genes was increased. The mean number of CyIIIa-CAT fusion genes per nucleus at which half saturation was obtained was 105 \u00b1 40 (mean \u00b1 SD). This result suggests that equilibrium parameters measured earlier in vitro may apply, at least approximately, within the embryo nuclei.", "pmcid": "PMC282241", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1988-10-15", "series_number": "20", "volume": "85", "issue": "20", "pages": "7607-7611" }, { "id": "authors:mfxcc-n7k16", "collection": "authors", "collection_id": "mfxcc-n7k16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160520-104219073", "type": "article", "title": "A regulatory domain that directs lineage-specific expression of a skeletal matrix protein gene in the sea urchin embryo", "author": [ { "family_name": "Sucov", "given_name": "Henry M.", "clpid": "Sucov-H-M" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Franks", "given_name": "Roberta R.", "clpid": "Franks-R-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "DNA sequences derived from the 5' region of a gene coding for the 50-kD skeletal matrix protein (SM50) of sea urchin embryo spicules were linked to the CAT reporter gene and injected into unfertilized eggs. CAT mRNA and enzyme were synthesized from these fusion constructs in embryos derived from these eggs, and in situ hybridization with a CAT antisense RNA probe demonstrated that expression is confined to skeletogenic mesenchyme cells. A mean of 5.5 of the 32-blastula-stage skeletogenic mesenchyme cells displayed CAT mRNA (range 1-15), a result consistent with earlier measurements indicating that incorporation of the exogenous injected DNA probably occurs in a single blastomere during early cleavage. In vitro mutagenesis and deletion experiments showed that CAT enzyme activity in the transgenic embryos is enhanced 34-fold by decreasing the number of SM50 amino acids at the amino-terminus of the fusion protein from 43 to 4. cis-regulatory sequences that are sufficient to promote lineage-specific spatial expression in the embryo are located between -440 and +120 with respect to the transcriptional initiation site.", "doi": "10.1101/gad.2.10.123", "issn": "0890-9369", "publisher": "Cold Spring Harbor Laboratory Press", "publication": "Genes and Development", "publication_date": "1988-10", "series_number": "10", "volume": "2", "issue": "10", "pages": "1238-1250" }, { "id": "authors:f2kxs-3zf61", "collection": "authors", "collection_id": "f2kxs-3zf61", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-093724850", "type": "article", "title": "Mosaic Incorporation and Regulated Expression of an Exogenous Gene in the Sea Urchin Embryo", "author": [ { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A fusion gene construct in which the bacterial chloramphenicol acetyltransferase (CAT) gene is controlled by CyIIIa actin gene cis-regulatory sequences was injected into unfertilized eggs of the sea urchin Strongylocentrotus purpuratus. The distribution of CAT DNA sequences was measured directly by in situ hybridization in squashed 24-hr blastula preparations derived from these eggs. Earlier studies had shown that stable mosaic incorporation of the exogenous DNA occurs during cleavage, after which the exogenous sequences replicate at approximately the pace of the host cell genomes. The fractions of embryonic cells observed in this study to include CAT DNA sequences imply that their stable incorporation into a replicating, nuclear form occurs most often in a single cell at the 3rd or 4th cleavage stages, though it may occur as early as 2nd cleavage, or as late as 7th cleavage. Corroborative measurements were carried out by the same method on squashed preparations of embryos at earlier stages, and by in situ hybridizations of CAT mRNA, both in dissociated embryos and in cytological sections of 72-hr pluteus-stage embryos. Hybridizations to CAT mRNA and to CAT DNA were carried out on alternate sections of several embryos. The results confirm unequivocally that although CAT mRNA appears only in the aboral ectoderm in embryos derived from eggs injected with the CyIIIa \u00b7 CAT fusion gene, the exogenous sequences are indeed present, though silent, in the various other cell types of the late embryo.", "doi": "10.1016/0012-1606(88)90174-1", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1988-09", "series_number": "1", "volume": "129", "issue": "1", "pages": "198-208" }, { "id": "authors:4jbsc-wsp52", "collection": "authors", "collection_id": "4jbsc-wsp52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160518-080831122", "type": "article", "title": "Developmental appearance of factors that bind specifically to cis-regulatory sequences of a gene expressed in the sea urchin embryo", "author": [ { "family_name": "Calzone", "given_name": "Frank J.", "clpid": "Calzone-F-J" }, { "family_name": "Th\u00e9z\u00e9", "given_name": "Nadine", "clpid": "Th\u00e9z\u00e9-N" }, { "family_name": "Thiebaud", "given_name": "Pierre", "clpid": "Thiebaud-P" }, { "family_name": "Hill", "given_name": "Ronald L.", "clpid": "Hill-R-L" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Previous gene-transfer experiments have identified a 2500-nucleotide 5' domain of the CyIIIa cytoskeletal actin gene, which contains cis-regulatory sequences that are necessary and sufficient for spatial and temporal control of CyIIIa gene expression during embryogenesis. This gene is activated in late cleavage, exclusively in aboral ectoderm cell lineages. In this study, we focus on interactions demonstrated in vitro between sequences of the regulatory domain and proteins present in crude extracts derived from sea urchin embryo nuclei and from unfertilized eggs. Quantitative gel-shift measurements are utilized to estimate minimum numbers of factor molecules per embryo at 24 hr postfertilization, when the CyIIIa gene is active, at 7 hr, when it is still silent, and in the unfertilized egg. We also estimate the binding affinity preferences (K_r) of the various factors for their respective sites, relative to their affinity for synthetic DNA competitors. At least 14 different specific interactions occur within the regulatory regions, some of which produce multiple DNA-protein complexes. Values of K_r range from approximately 2 x 10^4 to approximately 2 x 10^6 for these factors under the conditions applied. With one exception, the minimum factor prevalences that we measured in the 400-cell 24-hr embryo nuclear extracts fell within the range of 2 x 10^5 to 2 x 10^6 molecules per embryo, i.e., a few hundred to a few thousand molecules per nucleus. Three developmental patterns were observed with respect to factor prevalence: Factors reacting at one site were found in unfertilized egg cytoplasm at about the same level per egg or embryo as in 24-hr embryo nuclei; factors reacting with five other regions of the regulatory domain are not detectable in egg cytoplasm but in 7-hr mid-cleavage-stage embryo, nuclei are already at or close to their concentrations in the 24-hr embryo nuclei; and factors reacting with five additional regions are not detectable in egg cytoplasm and are low in 7-hr embryo nuclei, i.e., \u2a7d10% per embryo of the level they attain in 24-hr embryo nuclei. The rise in concentration of factors of the latter class could provide the proximal cause for the temporal activation of the CyIIIa gene at the early blastula stage.", "doi": "10.1101/gad.2.9.1074", "issn": "0890-9369", "publisher": "Cold Spring Harbor Laboratory Press", "publication": "Genes and Development", "publication_date": "1988-09", "series_number": "9", "volume": "2", "issue": "9", "pages": "1074-1088" }, { "id": "authors:x61jz-7km60", "collection": "authors", "collection_id": "x61jz-7km60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas88", "type": "article", "title": "Sources and evolution of human Alu repeated sequences", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Baron", "given_name": "Will F.", "clpid": "Baron-W-F" }, { "family_name": "Stout", "given_name": "David B.", "clpid": "Stout-D-B" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Alu repeated sequences arising in DNA of the human lineage during about the last 30 million years are closely similar to a modern consensus. Alu repeats arising at earlier times share correlated blocks of differences from the current consensus at diagnostic positions in the sequence. Using these 26 positions, we can recognize four subfamilies and the older ones are each successively closer to the 7SL sequence. It appears that there has existed a series of conserved genes that are the primary sources of the Alu repeat family, presumably through retroposition. These genes have probably replaced each other in overlapping relays during the evolution of primates.", "pmcid": "PMC280517", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1988-07-01", "series_number": "13", "volume": "85", "issue": "13", "pages": "4770-4774" }, { "id": "authors:4jeh2-pre87", "collection": "authors", "collection_id": "4jeh2-pre87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160520-112154892", "type": "article", "title": "A long, nontranslatable poly(A) RNA stored in the egg of the sea urchin Strongylocentrotus purpuratus", "author": [ { "family_name": "Calzone", "given_name": "Frank J.", "clpid": "Calzone-F-J" }, { "family_name": "Lee", "given_name": "James J.", "clpid": "Lee-J-J" }, { "family_name": "Le", "given_name": "Nga", "clpid": "Le-Nga" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Nontranslatable transcripts containing interspersed repetitive sequence elements constitute a major fraction of the poly(A) RNA stored in the cytoplasm of both the sea urchin egg and the amphibian oocyte. We report the first complete sequence of a representative interspersed maternal RNA transcript, called ISp1. The transcript is about 3.7 kb in length [including poly(A) tail]; and the 5' half consists of a cluster of repetitive sequences, whereas the 3' half is single copy. Other repetitive sequences occur in the 5' and 3' regions flanking the transcription unit. In several cloned alleles, the flanking repetitive and single-copy sequences differ, indicating a high degree of insertional and deletional rearrangement around, as well as within, the transcription unit. No significant open reading frames exist in any region of the ISp1 transcript, nor is it spliced to give rise to translatable mRNA in egg or embryo. A 620-nucleotide repetitive sequence element at the 5' end of the ISp1 transcript is also represented in a large number of other long interspersed maternal poly(A) RNAs. In addition, this sequence appears in a prevalent set of small polyadenylated RNAs about 600-nucleotides in length, which disappear almost completely by the gastrula stage of development. The structural features of the ISp1 RNA uncovered in this work exclude several hypotheses of interspersed maternal poly(A) RNA origin and function.", "doi": "10.1101/gad.2.3.305", "issn": "0890-9369", "publisher": "Cold Spring Harbor Laboratory Press", "publication": "Genes and Development", "publication_date": "1988-03", "series_number": "3", "volume": "2", "issue": "3", "pages": "305-318" }, { "id": "authors:vr48g-78947", "collection": "authors", "collection_id": "vr48g-78947", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:FRAdev88", "type": "article", "title": "Direct introduction of cloned DNA into the sea urchin zygote nucleus, and fate of injected DNA", "author": [ { "family_name": "Franks", "given_name": "Roberta R.", "clpid": "Franks-R-R" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A method is described for microinjection of cloned DNA into the zygote nucleus of Lytechinus variegatus. Eggs of this species are unusually transparent, facilitating visual monitoring of the injection process. The initial fate of injected DNA fragments appears similar to that observed earlier for exogenous DNA injected into unfertilized egg cytoplasm. Thus after end-to-end ligation, it is replicated after a lag of several hours to an extent indicating that it probably participates in most of the later rounds of DNA synthesis undergone by the host cell genomes during cleavage. The different consequences of nuclear versus cytoplasmic injection are evident at advanced larval stages. Larvae descendant from eggs in which exogenous DNA was injected into the nuclei are four times more likely (32% versus 8%) to retain this DNA in cell lineages that replicate very extensively during larval growth, i.e. the lineages contributing to the imaginal rudiment, and thus to display greatly enhanced contents of the exogenous DNA. Similarly, 36% of postmetamorphic juveniles from a nuclear injection sample retained the exogenous DNA sequences, compared to 12% of juveniles from a cytoplasmic injection sample. However, the number of copies of the exogenous DNA sequences retained per average genome in postmetamorphic juveniles was usually less than 0.1 (range 0.05-50), and genome blot hybridizations indicate that these sequences are organized as integrated, randomly oriented, end-to-end molecular concatenates. It follows that only a small fraction of the cells of the average juvenile usually retains the exogenous sequences. Thus, even when introduced by nuclear microinjection, the stable incorporation of exogenous DNA in the embryo occurs in a mosaic fashion, although in many recipients the DNA enters a wider range of cell lineages than is typical after cytoplasmic injection. Nuclear injection would probably be the route of choice for studies of exogenous DNA function in the postembryonic larval rudiment.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1988-02", "series_number": "2", "volume": "102", "issue": "2", "pages": "287-299" }, { "id": "authors:bhb40-7hy87", "collection": "authors", "collection_id": "bhb40-7hy87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160523-070013892", "type": "article", "title": "Spatially deranged though temporally correct expression of a Strongylocentrotus purpuratus actin gene fusion in transgenic embryos of a different sea urchin family", "author": [ { "family_name": "Franks", "given_name": "Roberta R.", "clpid": "Franks-R-R" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "We report the unexpected observation that cis-regulatory sequences of a Strongylocentrotus purpuratus actin gene, which direct a particular, lineage-specific pattern of embryonic expression, confer a completely different spatial pattern of expression when introduced into embryos of another sea urchin species. We utilized a fusion gene construct in which the bacterial chloramphenicol acetyl transferase (CAT) reporter gene is driven by CyIIIa actin regulatory sequences. We previously showed that the regulatory region that is included suffices to promote the accumulation of CAT mRNA in transgenic S. purpuratus embryos, on the same developmental schedule and in the same embryonic region, the aboral ectoderm, in which the CyIIIa actin gene is normally expressed (Flytzanis et al. 1987; Hough-Evans et al. 1987). When injected into zygotes of Lytechinus variegatus, which belongs to a different echinoid family, the expected temporal pattern of expression of CAT enzyme was observed. Thus, in both S. purpuratus and L. variegatus embryos, expression is activated at the early blastula stage, although this stage is attained several hours sooner in L. variegatus embryo cultures. Similar kinetics of CAT enzyme accumulation were obtained whether the gene was introduced directly into the L. variegatus zygote nucleus or into the cytoplasm. However, when examined by in situ hybridization, the transgenic L. variegatus embryos were found to display a totally new pattern of CAT mRNA accumulation. Copious CAT transcripts were detected not only in aboral ectoderm cells, but also in skeletogenic mesenchyme cells, gut cells, and oral ectoderm, all cell types that in the transgenic S. purpuratus controls are invariably devoid of detectable CAT transcripts.", "doi": "10.1101/gad.2.1.1", "issn": "0890-9369", "publisher": "Cold Spring Harbor Laboratory Press", "publication": "Genes and Development", "publication_date": "1988-01", "series_number": "1", "volume": "2", "issue": "1", "pages": "1-12" }, { "id": "authors:w9v42-ag180", "collection": "authors", "collection_id": "w9v42-ag180", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KATdev87", "type": "article", "title": "Ontogenic expression of a CyI actin fusion gene injected into sea urchin eggs", "author": [ { "family_name": "Katula", "given_name": "Karen S.", "clpid": "Katula-K-S" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The 5' terminus of the CyI actin gene transcription unit of Strongylocentrotus purpuratus was located by primer extension and other procedures, and the flanking upstream region was partially sequenced and mapped. A fusion gene was constructed containing about 2.5 kb of 5' flanking sequence, the transcribed leader sequence, and the first few codons of the CyI gene ligated to the bacterial gene coding for chloramphenicol acetyl transferase (CAT). This was micro-injected into the cytoplasm of S. purpuratus eggs, and CAT enzyme activity was measured at various stages of embryonic development. CAT synthesis was activated between 10 and 14 h postfertilization, the same time at which newly synthesized transcripts of the endogenous CyI gene first appear. The exogenous CyI.CAT fusion DNA replicated actively during cleavage, as observed previously for other DNAs injected into sea urchin egg cytoplasm. Thus the absence of CAT activity prior to 10 h postfertilization could not be due to insufficient CyI.CAT genes. The amounts of CAT enzyme produced by embryos bearing CyI.CAT deletions that lack various regions of the CyI sequence were measured. As little as 254 nucleotides of upstream CyI sequence suffice for correct temporal activation of the fusion construct, although the level of CAT enzyme produced in embryos bearing any deletion retaining less than 850 nucleotides of upstream sequence was significantly lowered compared to controls bearing the complete CyI.CAT fusion construct.", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "1987-11", "series_number": "3", "volume": "101", "issue": "3", "pages": "437-447" }, { "id": "authors:1b4fp-9m389", "collection": "authors", "collection_id": "1b4fp-9m389", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-093724349", "type": "article", "title": "Expression of Myosin Heavy Chain Gene in the Sea Urchin: Coregulation with Muscle Actin Transcription in Early Development", "author": [ { "family_name": "Rose", "given_name": "Samuel J.", "clpid": "Rose-S-J" }, { "family_name": "Rosenberg", "given_name": "Marvin J.", "clpid": "Rosenberg-M-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A fragment of a Strongylocentrotus purpuratus (Sp) myosin heavy chain (MHC) gene was isolated from a genomic recombinant DNA library by cross-reaction with a cloned Drosophila melanogaster (Dm) MHC probe. A portion of a 227-nucleotide Sp coding sequence that is included in this fragment predicts a peptide very closely homologous with a region of the Dm sequence. The MHC gene sequence is present in a single copy per haploid Sp genome, and the gene is utilized in adult as well as embryonic muscle. The quantity of MHC transcript was measured in embryos of various stages by single-strand RNA probe excess titration. Transcripts are not observed until postgastrular stages, after which they accumulate rapidly. The time course of accumulation closely parallels that measured earlier for muscle actin message.", "doi": "10.1016/0012-1606(87)90433-7", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1987-09", "series_number": "1", "volume": "123", "issue": "1", "pages": "115-124" }, { "id": "authors:r8eq8-xpk26", "collection": "authors", "collection_id": "r8eq8-xpk26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160412-142332974", "type": "article", "title": "Sea Urchin Actin Gene Linkages Determined by Genetic Segregation", "author": [ { "family_name": "Minor", "given_name": "Joseph E.", "clpid": "Minor-J-E" }, { "family_name": "Lee", "given_name": "James J.", "clpid": "Lee-J-J" }, { "family_name": "Akhurst", "given_name": "Rosemary J.", "clpid": "Akhurst-R-J" }, { "family_name": "Leahy", "given_name": "Patrick S.", "clpid": "Leahy-P-S" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Genetic linkage between the actin genes of Strongylocentrotus purpuratus was investigated by observing the segregation of restriction fragment length polymorphisms (RFLPs). Specific RFLPs of actin gene pairs CyICyIIa and CyIIIaCyIIIb always cosegregated, confirming the linkage groups CyI-CyIIa-CyIIb and CyIIIa-CyIIIb previously determined by molecular cloning. In contrast, RFLPs of actin genes CyICyIIa, CyIIIaCyIIIb, and M all segregated at random with respect to one another. This demonstrates that the known actin gene clusters CyI-CyIIa-CyIIb, CyIIIa-CyIIIb, and the M actin gene are not closely linked.", "doi": "10.1016/0012-1606(87)90354-X", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1987-07", "series_number": "1", "volume": "122", "issue": "1", "pages": "291-295" }, { "id": "authors:0x526-e3f85", "collection": "authors", "collection_id": "0x526-e3f85", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121023-100217450", "type": "article", "title": "Correct Cell-Type-Specific Expression of a Fusion Gene\n Injected into Sea Urchin Eggs", "author": [ { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Franks", "given_name": "Roberta R.", "clpid": "Franks-R-R" }, { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A fusion gene construct containing the bacterial chloramphenicol acetyltransferase (CAT) gene under the control of CyIIIa actin gene regulatory sequences was injected into unfertilized eggs of the sea urchin Strongylocentrotus purpuratus, and early pluteus stage embryos that developed from these eggs were fixed and sectioned for analysis by in situ hybridization. A [^3H]RNA antisense probe for CAT mRNA was hybridized to 5-\u03bcm embryo sections. Autoradiographic signal denoting the presence of CAT mRNA was detected only over aboral ectoderm cells, in which the CyIIIa gene is normally expressed, and not over any recognizable regions of gut or oral ectoderm included in the same sections.", "doi": "10.1016/0012-1606(87)90193-X", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1987-06", "series_number": "2", "volume": "121", "issue": "2", "pages": "576-579" }, { "id": "authors:2jx43-mkn18", "collection": "authors", "collection_id": "2jx43-mkn18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-085616444", "type": "article", "title": "A Lineage-Specific Gene Encoding a Major Matrix Protein of the Sea Urchin Embryo Spicule: II. Structure of the Gene and Derived Sequence of the Protein", "author": [ { "family_name": "Sucov", "given_name": "Henry M.", "clpid": "Sucov-H-M" }, { "family_name": "Benson", "given_name": "Steve", "clpid": "Benson-S" }, { "family_name": "Robinson", "given_name": "John J.", "clpid": "Robinson-J-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Wilt", "given_name": "Fred", "clpid": "Wilt-F" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A \u03bbgt11 cDNA clone isolated by use of a polyclonal antispicule matrix protein antiserum is shown in the accompanying paper [S. C. Benson, H. M. Sucov, L. Stephens, E. H. Davidson, and F. Wilt (1987) Dev. Biol.120, 499\u2013506] to encode a prominent 50-kDa spicule matrix protein (SM50). This clone was used to select homologous genomic recombinants, and the structure of the gene was determined. The SM50 gene occurs once per haploid genome. It contains a single intron located within the 35th codon. A unique transcription initiation site 110 nucleotide pairs prior to the translation start signal was mapped by primer extension. The mRNA is 1895 nucleotides in length, excluding the 3\u2032 poly(A) sequence, and contains a single open reading frame 450 codons in length. Though rare in whole embryo RNA the prevalence of the SM50 mRNA is calculated to be about 1% of the total mRNA in skeletogenic mesenchyme cells. The derived peptide sequence indicates a typical N-terminal signal peptide, and an N-linked glycosylation site near the C terminus. About 45% of the length of the protein is included in a domain composed of consecutive approximate repetitions of a 13-aminoacid element, the consensus sequence of which is\nTrp-Val-Gly-Asp-Asn-Gln-Ala-^(Leu)_(Trp)-Val-^(Ile)_(Asp)-Asn-^(Gln-Val)_(Pro-Glu). The protein also contains an internal domain unusually rich in proline residues and a very basic C-terminal region.", "doi": "10.1016/0012-1606(87)90254-5", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1987-04", "series_number": "2", "volume": "120", "issue": "2", "pages": "507-519" }, { "id": "authors:zrtv4-z5w29", "collection": "authors", "collection_id": "zrtv4-z5w29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-095801104", "type": "article", "title": "Structure and organization of the CyIII actin gene subfamily of the sea urchin, Strongylocentrotus purpuratus", "author": [ { "family_name": "Akhurst", "given_name": "Rosemary J.", "clpid": "Akhurst-R-J" }, { "family_name": "Calzone", "given_name": "Frank J.", "clpid": "Calzone-F-J" }, { "family_name": "Lee", "given_name": "James J.", "clpid": "Lee-J-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "We describe here the organization of the CyIII subfamily of cytoskeletal actin genes in the sea urchin Strongylocentrotus purpuratus. The functional genes CyIIIa and CyIIIb are linked at a 6 \u00d7 10^3-base distance. Gene CyIIIc appears to be a pseudogene that lacks 5\u2032 exons and displays unselected mutational changes. Gene CyIIIa codes for a protein that differs at only nine out of 376 residues from that coded by another cytoskeletal actin gene, CyI. However, five of these nine changes occur within an 11-amino acid region that could represent a functional specialization of the CyIIIa actin protein. The CyIIIa gene possesses three introns, located, respectively, 25 nucleotides upstream from the translation start site, between the codons for amino acids 121 and 122, and within the codon for amino acid 204. These intron positions have also been observed in other cytoskeletal sea urchin actin genes. Comparison of both intron and 3\u2032-terminal sequences shows that the CyIIIa and CyIIIb genes are closely related, while no homology in these untranslated sequences is observed between the CyIII genes and the other cytoskeletal actin genes of the S. purpuratus genome. The CyIII genes probably arose by duplication events at least 40 \u00d7 10^6 years ago, prior to radiation of the genus Strongylocentrotus. Consideration of the biological role of the embryo and larval aboral ectoderm cells to which CyIIIa and CyIIIb transcripts are confined suggests that these actins might contribute to cytoskeletal elements that endow the larval body wall with its rigid structure.", "doi": "10.1016/0022-2836(87)90368-8", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1987-03-20", "series_number": "2", "volume": "194", "issue": "2", "pages": "193-203" }, { "id": "authors:5z892-aa331", "collection": "authors", "collection_id": "5z892-aa331", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121023-083116845", "type": "article", "title": "Lineage and fate of each blastomere of the eight-cell sea urchin embryo", "author": [ { "family_name": "Cameron", "given_name": "R. Andrew", "orcid": "0000-0003-3947-6041", "clpid": "Cameron-R-A-Bio" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A fluoresceinated lineage tracer was injected into individual blastomeres of eight-cell sea urchin (Strongylocentrotus purpuratus) embryos, and the location of the progeny of each blastomere was determined in the fully developed pluteus. Each blastomere gives rise to a unique portion of the advanced embryo. We confirm many of the classical assignments of cell fate along the animal-vegetal axis of the cleavage-stage embryo, and demonstrate that one blastomere of the animal quartet at the eight-cell stage lies nearest the future oral pole and the opposite one nearest the future aboral pole of the embryo. Clones of cells deriving from ectodermal founder cells always remain contiguous, while clones of cells descendant from the vegetal plate (i.e., gut, secondary mesenchyme) do not. The locations of ectodermal clones contributed by specific blastomeres require that the larval plane of bilateral symmetry lie approximately equidistant (i.e., at a 45 degree angle) from each of the first two cleavage planes. These results underscore the conclusion that many of the early spatial patterns of differential gene expression observed at the molecular level are specified in a clonal manner early in embryonic sea urchin development, and are each confined to cell lineages established during cleavage.", "doi": "10.1101/gad.1.1.75", "issn": "0890-9369", "publisher": "Cold Spring Harbor Laboratory Press", "publication": "Genes and Development", "publication_date": "1987-03", "series_number": "1", "volume": "1", "issue": "1", "pages": "75-84" }, { "id": "authors:fv55b-tvd50", "collection": "authors", "collection_id": "fv55b-tvd50", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:FLYpnas87", "type": "article", "title": "Ontogenic activation of a fusion gene introduced into sea urchin eggs", "author": [ { "family_name": "Flytzanis", "given_name": "Constantin N.", "clpid": "Flytzanis-C-N" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Regulatory sequences of a sea urchin cytoskeletal actin gene (CyIIIa) were ligated to the bacterial gene coding for chloramphenicol acetyltransferase (CAT; acetyl-CoA:chloramphenicol O3-acetyltransferase, EC 2.3.1.28) and the construct was injected into unfertilized sea urchin eggs. CAT activity is detected at the early blastula stage, when transcripts of the endogenous CyIIIa gene normally appear. Our measurements show that during activation the amount of CAT enzyme increases at least 100-fold; that there are present in late blastula stage embryos about 5 x 105 molecules of CAT mRNA (i.e., \u22486 times the number of endogenous CyIIIa mRNAs); and that within the range studied the amount of CAT enzyme produced is independent of the number of CyIIIa-CAT genes incorporated per embryo, probably because the genes are present in excess of factors required for their activation. Activation of the CyIIIa-CAT construct is seriously inhibited, or abolished, by successive deletions of upstream CyIIIa sequences.", "doi": "10.1073/pnas.84.1.151", "pmcid": "PMC304160", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1987-01", "series_number": "1", "volume": "84", "issue": "1", "pages": "151-155" }, { "id": "authors:pvmgh-s6n32", "collection": "authors", "collection_id": "pvmgh-s6n32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GAOpnas86", "type": "article", "title": "Sequence of mRNA Coding for Bindin, a Species-Specific Sea Urchin Sperm Protein Required for Fertilization", "author": [ { "family_name": "Gao", "given_name": "Boning", "clpid": "Gao-Boning" }, { "family_name": "Klein", "given_name": "Laurie E.", "clpid": "Klein-L-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Bindin, a major protein of the sea urchin acrosome granule, mediates the species-specific adhesion and binding of sperm to egg required to effect fertilization. We report the isolation and sequence of bindin cDNA clones prepared from Strongylocentrotus purpuratus testis RNA. The bindin gene appears to be productively expressed only in males and only in testes. The protein is produced from a 51-kDa precursor, which is subsequently processed to yield the mature 24-kDa bindin protein.", "pmcid": "PMC386985", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1986-11-15", "series_number": "22", "volume": "83", "issue": "22", "pages": "8634-8638" }, { "id": "authors:8z2z4-3vd54", "collection": "authors", "collection_id": "8z2z4-3vd54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HWUpnas86", "type": "article", "title": "Insertion and/or Deletion of Many Repeated DNA Sequences in Human and Higher Ape Evolution", "author": [ { "family_name": "Hwu", "given_name": "Huey Ru", "clpid": "Hwu-Huey-Ru" }, { "family_name": "Roberts", "given_name": "John W.", "clpid": "Roberts-J-W" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The total numbers of copies of two repeat families, L1 (Kpn I) and Alu, have been measured in the DNA of four higher apes by an accurate titration method. The number of members of the Alu family repeats in the four genomes are as follows: human, 910,000; chimpanzee, 330,000; gorilla, 410,000; orangutan, 580,000. For the Kpn I family (3'-ward higher frequency region) the number of copies in these genomes are as follows: human, 107,000; chimpanzee, 51,000; gorilla, 64,000; orangutan, 84,000. Thermal stability measurements show that, although the families of repeats are moderately divergent in sequence, little net sequence change has occurred during the evolution of the higher apes. Most or all of the members of these families of repeats are interspersed throughout the genome. Therefore, a large number of events of insertion and/or deletion of these DNA sequences has occurred during higher primate evolution.", "pmcid": "PMC323627", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1986-06-01", "series_number": "11", "volume": "83", "issue": "11", "pages": "3875-3879" }, { "id": "authors:j72nm-egz17", "collection": "authors", "collection_id": "j72nm-egz17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-120131159", "type": "article", "title": "Rates of DNA sequence evolution differ between taxonomic groups", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The mutation rates of DNA sequences during evolution can be estimated from interspecies DNA sequence differences by assaying changes that have little or no effect on the phenotype (neutral mutations). Examination of available measurements shows that rates of DNA change of different phylogenetic groups differ by a factor of 5. The slowest rates are observed for higher primates and some bird lineages, while faster rates are seen in rodents, sea urchins, and drosophila. The rate of DNA sequence change has decreased markedly during primate evolution. The contrast in rates of DNA sequence change is probably due to evolutionary variation and selection of biochemical mechanisms such as DNA replication or repair.", "doi": "10.1126/science.3082006", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1986-03-21", "series_number": "4744", "volume": "231", "issue": "4744", "pages": "1393-1398" }, { "id": "authors:yqm2n-3bt58", "collection": "authors", "collection_id": "yqm2n-3bt58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-093631911", "type": "article", "title": "Activation of sea urchin actin genes during embryogenesis: Measurement of transcript accumulation from five different genes in Strongylocentrotus purpuratus", "author": [ { "family_name": "Lee", "given_name": "James J.", "clpid": "Lee-J-J" }, { "family_name": "Calzone", "given_name": "Frank J.", "clpid": "Calzone-F-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Angerer", "given_name": "Robert C.", "clpid": "Angerer-R-C" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The number of molecules of mRNA transcribed from each of five different actin genes are reported for developing embryos of the sea urchin Strongylocentrotus purpuratus. Transcripts of the cytoskeletal actin genes CyI, CyIIa, CyIIb and CyIIIa, and of the muscle actin gene M, were measured in unfertilized egg and embryo RNAs of cleavage, blastula, gastrula and pluteus stages. The measurements were obtained by probe excess titrations of these RNAs, using a set of single-stranded RNA probes each identifying the mRNA transcripts of a specific actin gene. These mRNAs can be identified by their distinct 3\u2032 non-translated trailer sequences. We confirm prior observations that the prevalence of actin mRNA in the unfertilized egg is low. Cytoskeletal actin genes CyI and CyIIIa each contribute 1 \u00d7 10^3 to 2 \u00d7 10^3 maternal mRNA molecules, and CyIIb contributes < 2 \u00d7 10^2 mRNA molecules, while no detectable maternal mRNAs derive from cytoskeletal actin gene CyIIa or the muscle actin gene M. During certain periods of development, transcripts derived from the individual cytoskeletal actin genes accumulate rapidly, with kinetics specific to each mRNA. Transcripts of the muscle actin gene are absent until after gastrulation, when the initial muscle progenitor cells are formed. At late stages of development, each of the five genes studied is represented by 10^4 to 10^5 mRNA molecules per embryo. The present measurements permit calculation of the levels of each actin mRNA species in the particular cell types in which each gene functions in the fully differentiated embryo.", "doi": "10.1016/0022-2836(86)90302-5", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1986-03-20", "series_number": "2", "volume": "188", "issue": "2", "pages": "173-183" }, { "id": "authors:qcb15-eqn07", "collection": "authors", "collection_id": "qcb15-eqn07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151217-183243524", "type": "article", "title": "Evolutionary conservation of DNA sequences expressed in sea urchin eggs and early embryos", "author": [ { "family_name": "Roberts", "given_name": "John W.", "clpid": "Roberts-J-W" }, { "family_name": "Johnson", "given_name": "Steven A.", "orcid": "0000-0001-9397-4768", "clpid": "Johnson-S-A" }, { "family_name": "Kier", "given_name": "Porter", "clpid": "Kier-P" }, { "family_name": "Hall", "given_name": "Terrence J.", "clpid": "Hall-T-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "DNA sequence divergence measurements indicate that Strongylocentrotus franciscanus is more distinct from S. purpuratus and S. drobachiensis than these two species are from each other, in agreement with paleontological and morphological evidence. The evolutionary divergence of several classes of expressed DNA sequences was compared with that of total single-copy DNA. Between S. franciscanus and S. purpuratus the divergence of cDNA made from gastrula cytoplasmic poly(A)+ RNA is about half that of total single-copy DNA. Similar results were obtained for cDNA made from unfertilized egg poly(A)+ RNA. In contrast, sequences expressed in gastrula nuclear RNA have diverged almost as much as total single-copy DNA.", "doi": "10.1007/BF02101688", "issn": "0022-2844", "publisher": "Springer Verlag", "publication": "Journal of Molecular Evolution", "publication_date": "1985-10", "series_number": "2", "volume": "22", "issue": "2", "pages": "99-107" }, { "id": "authors:t3fgd-b4258", "collection": "authors", "collection_id": "t3fgd-b4258", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-080123212", "type": "article", "title": "Persistence and Integration of Cloned DNA in Postembryonic Sea Urchins", "author": [ { "family_name": "Flytzanis", "given_name": "Constantin N.", "clpid": "Flytzanis-C-N" }, { "family_name": "McMahon", "given_name": "Andrew P.", "orcid": "0000-0002-3779-1729", "clpid": "McMahon-Andrew-P" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Katula", "given_name": "Karen S.", "clpid": "Katula-K-S" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Cloned DNA was injected into the cytoplasm of unfertilized sea urchin eggs which were then fertilized and cultured in the laboratory through metamorphosis. The exogenous DNA replicated manyfold and persisted for weeks in a majority of growing larvae, as shown by hydridizing \"dot blots\" of the DNA of single individuals with appropriate labeled probes. After metamorphosis 5\u201315% of the juvenile sea urchins retained the exogenous sequences. Genomic integration of the exogenous sequence was observed in the DNA of a postmetamorphosis juvenile.", "doi": "10.1016/0012-1606(85)90046-6", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1985-04", "series_number": "2", "volume": "108", "issue": "2", "pages": "431-442" }, { "id": "authors:jjxs7-m6919", "collection": "authors", "collection_id": "jjxs7-m6919", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-080122940", "type": "article", "title": "Introduction of Cloned DNA into Sea Urchin Egg Cytoplasm: Replication and Persistence during Embryogenesis", "author": [ { "family_name": "McMahon", "given_name": "Andrew P.", "orcid": "0000-0002-3779-1729", "clpid": "McMahon-Andrew-P" }, { "family_name": "Flytzanis", "given_name": "Constantin N.", "clpid": "Flytzanis-C-N" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Katula", "given_name": "Karen S.", "clpid": "Katula-K-S" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "

Cloned DNA sequences were introduced into the cytoplasm of unfertilized sea urchin eggs by a simple microinjection technique. Sperm was then added, and development allowed to proceed. If linearized plasmids are injected they form random concatenates, and during the early development of the embryos replicate repeatedly. Eukaryotic sequences are not required for replication of the exogenous DNA. Injected supercoiled DNAs neither ligate nor replicate. Both forms of exogenous DNA persist in the embryo through pluteus stage.

", "doi": "10.1016/0012-1606(85)90045-4", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1985-04", "series_number": "2", "volume": "108", "issue": "2", "pages": "420-430" }, { "id": "authors:1thy8-nch27", "collection": "authors", "collection_id": "1thy8-nch27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MCMpnas84", "type": "article", "title": "Inducible expression of a cloned heat shock fusion gene in sea urchin embryos", "author": [ { "family_name": "McMahon", "given_name": "A. P.", "orcid": "0000-0002-3779-1729", "clpid": "McMahon-Andrew-P" }, { "family_name": "Novak", "given_name": "T. J.", "clpid": "Novak-T-J" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" } ], "abstract": "A fusion gene construct, in which the coding sequence for bacterial chloramphenicol acetyltransferase (CAT; acetyl-CoA: chloramphenicol 3-O-acetyltransferase, EC 2.3.1.28) was placed under the control of the regulatory region of the Drosophila gene encoding the 70-kilodalton heat shock protein [Di Nocera, P. P. & Dawid, I. B. (1983) Proc. Natl. Acad. Sci. USA 80, 7095-7098], was microinjected into the cytoplasm of unfertilized sea urchin eggs. Pluteus-stage embryos developing from the injected eggs were exposed to high temperature conditions that we found would elicit an endogenous sea urchin heat shock response. These embryos express the gene for CAT and, after heat treatment, display 8-10 times more CAT enzyme activity than do extracts from control embryos cultured at normal temperatures. The injected DNA is present in high molecular weight concatenates and, during development, is amplified about 100-fold. Amplified sequences are responsible for all or most of the induced CAT enzyme activity.", "pmcid": "PMC392172", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1984-12-01", "series_number": "23", "volume": "81", "issue": "23", "pages": "7490-7494" }, { "id": "authors:te02w-pq609", "collection": "authors", "collection_id": "te02w-pq609", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151217-182447236", "type": "article", "title": "Insertion of a short repetitive sequence (D881) in a sea urchin gene: A typical interspersed repeat?", "author": [ { "family_name": "Johnson", "given_name": "Steven A.", "orcid": "0000-0001-9397-4768", "clpid": "Johnson-S-A" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "A comparison has been made between the Sp88 gene regions of the DNAs of the sea urchins Strongylocentrotus purpuratus (Sp.) and Strongylocentrotus drobachiensis (Sd.). Examination of the 3\u2032 terminal part of the transcribed region revealed a short repetitive sequence present in Sd. but absent from Sp. A 12-nucleotide sequence present once in Sp. is almost perfectly duplicated at both ends of the repeat in Sd., suggesting that a mobile repeat was inserted in the Sd. genome. Other members of this family of repeated sequences occur in many interspersed locations in the genomes of both species. Except for the insertion duplication, the inserted sequence lacks direct or reverse repeats.", "doi": "10.1007/BF02104726", "issn": "0022-2844", "publisher": "Springer Verlag", "publication": "Journal of Molecular Evolution", "publication_date": "1984-08", "series_number": "3-4", "volume": "20", "issue": "3-4", "pages": "195-201" }, { "id": "authors:5vhqg-ct783", "collection": "authors", "collection_id": "5vhqg-ct783", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-070442729", "type": "article", "title": "Proteins of the Sea Urchin Egg Vitelline Layer", "author": [ { "family_name": "Niman", "given_name": "H. L.", "clpid": "Niman-H-L" }, { "family_name": "Hough-Evans", "given_name": "B. R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Vacquier", "given_name": "V. D.", "clpid": "Vacquier-V-D" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Lerner", "given_name": "R. A.", "clpid": "Lerner-R-A" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" } ], "abstract": "The vitelline layers (VL) of unfertilized sea urchin eggs were isolated, and the diversity of their polypeptide constitutents estimated by two-dimensional polyacrylamide gel electrophoresis. At least 25 components are reproducibly observed. While VL polypeptides are almost certainly synthesized in the growing oocyte, they are not among the more prevalent newly synthesized proteins detected in oocytes that were isolated and labeled in vitro for 4 hr. A set of monoclonal antibodies was raised against VL components and partially characterized. The 31 monoclonals analyzed fell into 11 classes with respect to their avidity for VL proteins solubilized under mild and under strongly denaturing conditions, and to their reactions with surface components of the VLs of living eggs. Fluorescence microscopy showed diverse patterns of surface reactivity when different monoclonal antibodies were compared. Two of the monoclonal antibodies reacted with specific sets of three proteins each on VL protein blots. It is concluded that the VL is a complex structure containing a large number of different polypeptide components, the genes for several of which should now be experimentally accessible.", "doi": "10.1016/0012-1606(84)90203-3", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1984-04", "series_number": "2", "volume": "102", "issue": "2", "pages": "390-401" }, { "id": "authors:6ebyw-avd62", "collection": "authors", "collection_id": "6ebyw-avd62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-090917087", "type": "article", "title": "Regulation of cytoplasmic mRNA prevalence in sea urchin embryos: Rates of appearance and turnover for specific sequences", "author": [ { "family_name": "Cabrera", "given_name": "Carlos V.", "clpid": "Cabrera-C-V" }, { "family_name": "Lee", "given_name": "James J.", "clpid": "Lee-J-J" }, { "family_name": "Ellison", "given_name": "Jay W.", "clpid": "Ellison-J-W" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Complementary DNA clones representing cytoplasmic poly(A) RNAs of sea urchin embryos were hybridized with metabolically labeled cytoplasmic RNA preparations and the rates of appearance and of decay for each transcript species were determined at the blastula-gastrula stage of development. The prevalence of the transcripts chosen for this study ranged, on average, from about one molecule per cell to a few hundred molecules per cell. The embryos were labeled continuously for 18 hours with [^3H]guanosine, beginning at 24 hours post-fertilization. The amount of cytoplasmic [^3H]poly(A) RNA that hybridized to each cloned sequence was determined and the specific activity of the [^3H]GTP pool was measured in the same embryos. Rate constants for the entry of each transcript species into the cytoplasm, and for its decay were extracted from these data. The embryo transcript species identified by the cloned probes displayed a range of stabilities. Half-lives of only a few hours were measured both for a very rare sequence and for a moderately prevalent sequence. Other newly synthesized transcripts, including sequences that first appear during embryonic development, as well as sequences also represented in maternal RNA, are far more stable. We conclude that cytoplasmic RNA turnover rate is a major variable in the determination of the cytoplasmic level of expression of embryo genes. The entry rates of the transcripts into the cytoplasm also varied, from a few molecules per embryo per minute to several hundred, depending on the sequence. By comparing the mass of transcripts of a given sequence in the embryo to the mass of transcripts of that sequence accumulating as a result of new synthesis, the point at which embryo transcription accounts for the major fraction of the cytoplasmic molecules could be estimated. This calculation showed that for some sequences maternal transcripts persist well beyond gastrulation, while other embryo poly(A) RNA species are largely the product of transcription in the embryo nuclei from the blastula stage onwards. There is no single stage at which all maternal transcripts are suddenly replaced by newly synthesized embryo transcripts. Primary transcription rates were measured for two sequences by determining accumulation of label in these RNA species soon after addition of [^3H]guanosine to the cultures. Comparing these rates to the cytoplasmic entry rates, we did not detect a significantly greater nuclear transcription of the sequence homologous to the cloned probe.", "doi": "10.1016/0022-2836(84)90366-8", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1984-03-25", "series_number": "1", "volume": "174", "issue": "1", "pages": "85-111" }, { "id": "authors:m37tt-nh285", "collection": "authors", "collection_id": "m37tt-nh285", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160412-144315585", "type": "article", "title": "Differential Expression of the Actin Gene Family of Strongylocentrotus purpuratus", "author": [ { "family_name": "Shott", "given_name": "Rosemary J.", "clpid": "Shott-R-J" }, { "family_name": "Lee", "given_name": "James J.", "clpid": "Lee-J-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Molecular probes that individually recognize the 3\u2032 nontranslated regions of six actin genes were utilized in RNA gel blot hybridizations to detect RNAs complementary to each gene in embryonic and adult tissues of Stronglyocentrotus purpuratus. In addition the probes were used in DNA excess filter hybridizations to estimate the relative contribution of the different actin genes. All six genes produce relatively stable mRNAs, and each displays a characteristic and distinct pattern of expression. On the basis of their expression in the egg, early embryos, or in adult coelomocytes, it is concluded that genes termed CyI, CyIIa, CyIIb, CyIIIa, and CyIIIb encode cytoskeletal actin proteins. Actin gene M gives rise to mRNAs that are found only in tissues containing muscle. Actin genes CyI, CyIIa, CyIIb, and M are expressed in both adult and embryonic tissues, giving rise to transcripts 2.1\u20132.2 kb in length. Expression of genes CyIIIa and CyIIIb is confined to the embryo. Gene CyIIIa provides the major embryonic actin mRNA, which is 1.8 kb in length. Three of the cytoskeletal actin genes are linked over a 30-kb distance in the S. purpuratus genome. We show that the actin genes included in this linkage group are not coordinately expressed.", "doi": "10.1016/0012-1606(84)90143-X", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1984-02", "series_number": "2", "volume": "101", "issue": "2", "pages": "295-306" }, { "id": "authors:c6hmb-z6y77", "collection": "authors", "collection_id": "c6hmb-z6y77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160518-084756331", "type": "article", "title": "Sea urchin actin gene subtypes", "author": [ { "family_name": "Lee", "given_name": "James J.", "clpid": "Lee-J-J" }, { "family_name": "Shott", "given_name": "Rosemary J.", "clpid": "Shott-R-J" }, { "family_name": "Rose", "given_name": "Samuel J.", "clpid": "Rose-S-J" }, { "family_name": "Thomas", "given_name": "Terry L.", "clpid": "Thomas-T-L" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The actin gene family of the sea urchin Strongylocentrotus purpuratus was analyzed by the genome blot method, using subcloned probes specific to the 3\u2032 terminal non-translated actin gene sequence, intervening sequence and coding region probes. We define an actin gene subtype as that gene or set of genes displaying homology with a given 3\u2032 terminal sequence probe, when hybridized at 55\u00b0C, 0\u00b775 m-Na+. By determining the often polymorphic restriction fragment band pattern displayed in genome blots by each probe, all, or almost all of the actin genes in this species could be classified. Our evidence shows that the S. purpuratus genome probably contains seven to eight actin genes, and these can be assigned to four subtypes. Studies of the expression of the genes (Shott et al., 1983) show that the actin genes of three of these subtypes code for cytoskeletal actins (Cy), while the fourth gives rise to a muscle-specific actin (M). We denote the array of S. purpuratus actin genes indicated by our data as follows. There is a single CyI actin gene, two or possibly three CyII genes (CyIIa, CyIIb, and possibly CyIIc), three CyIII actin genes (CyIIIa, CyIIIb, CyIIIc), and a single M actin gene. Comparative studies were carried out on the actin gene families of five other sea urchin species. At least the CyIIa and CyIIb genes are also linked in the Strongylocentrotus franciscanus genome, and this species also has a CyI gene, an M actin gene and at least two CyIII actin genes. It is not clear whether it also possesses a CyIIc actin gene, or a CyIIIc actin gene. The genome of a more closely related congener, Strongylocentrotus dr\u00f6bachiensis, includes 3\u2032 terminal sequences suggesting the presence of a CyIIc gene. In S. franciscanus and S. dr\u00f6bachiensis the first intron of the CyI gene has remained homologous with intron sequences of both the CyIIa and CyIIb genes, indicating a common origin of these three linked cytoskeletal actin genes. Of the four S. purpuratus 3\u2032 terminal subtype probe sequences only the CyI 3\u2032 terminal sequence has been conserved sufficiently during evolution to permit detection outside of the genus Strongylocentrotus. An unexpected observation was that a sequence found only in the 3\u2032 untranslated region of the CyII actin gene in the DNA of S. dr\u00f6bachiensis and S. purpuratus is represented as a large family of interspersed repeat sequences in the genome of S. franciscanus.", "doi": "10.1016/S0022-2836(84)80035-2", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1984-01-15", "series_number": "2", "volume": "172", "issue": "2", "pages": "149-176" }, { "id": "authors:9yrkj-g3d33", "collection": "authors", "collection_id": "9yrkj-g3d33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ROBpnas83", "type": "article", "title": "Comparison of sea urchin and human mtDNA: Evolutionary rearrangement", "author": [ { "family_name": "Roberts", "given_name": "John W.", "clpid": "Roberts-J-W" }, { "family_name": "Grula", "given_name": "John W.", "clpid": "Grula-J-W" }, { "family_name": "Posakony", "given_name": "James W.", "clpid": "Posakony-J-W" }, { "family_name": "Hudspeth", "given_name": "Richard", "clpid": "Hudspeth-R-L" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Clones of full-length mtDNA have been isolated from a Strongylocentrotus franciscanus recombinant DNA library by secreening a cDNA clone of cytochrome oxidase subunit 1 mRNA. Restriction fragment cross-hybridization analysis shows the following difference in gene arrangement between sea urchin and human mtDNA. The 16S rRNA and cytochrome oxidase subunit 1 genes are directly adjacent in sea urchin mtDNA. These two genes are separated in human and other mammalian mtDNAs by the region containing unidentified reading frames 1 and 2. In spite of the difference in gene order, gene polarity appears to have been conserved. We conclude that the difference in gene order reflects a rearrangement that took place in the sea urchin lineage since sea urchins and mammals last shared a common ancestor.", "pmcid": "PMC384094", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1983-08-01", "series_number": "15", "volume": "80", "issue": "15", "pages": "4614-4618" }, { "id": "authors:brgbx-9rs77", "collection": "authors", "collection_id": "brgbx-9rs77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-111340734", "type": "article", "title": "Interspersed sequence organization and developmental representation of cloned poly(A) RNAs from sea urchin eggs", "author": [ { "family_name": "Posakony", "given_name": "James W.", "clpid": "Posakony-J-W" }, { "family_name": "Flytzanis", "given_name": "Constantin N.", "clpid": "Flytzanis-C-N" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A random primed complementary DNA (cDNA) clone library constructed from total maternal poly(A) RNA of sea urchin eggs was screened with two cloned genomic repetitive sequence probes. Sets of cDNA clones reacting with each of these repetitive sequences were recovered. Most of the cloned transcripts included both single copy and repeat sequence elements. Except for the shared repeat sequence element, both the repetitive and single copy regions of the members of each set of clones failed to crossreact. Single copy probes linked to the repeats on the cloned maternal RNAs are represented in an asymmetric manner. It follows that many different genomic members of a given dispersed repeat sequence family are represented in the maternal RNA. RNA gel blots carried out with several repeat probes display about 10 to 20 prominent maternal poly(A) RNAs containing transcripts of each repetitive sequence family. The interspersed maternal transcripts are 3000 to 15,000 bases in length. Maternal transcripts reacting with single copy probes derived from the cloned cDNAs persist during embryonic development, and in some cases appear to be augmented by similar, newly synthesized embryo transcripts. Two examples were found in which additional transcripts of different length appear at specific developmental stages. The transcribed single copy regions are highly polymorphic in the genomes of different individual sea urchins, and comparisons of closely related sea urchin species showed that both the prevalence and length of specific maternal transcripts change rapidly during evolution. Nucleotide sequences of two homologous repeat elements occurring on different cloned transcripts displayed translation stop codons in every possible reading frame. These repeat sequences display structural features suggesting that there has been evolutionary transposition into transcription units active during oogenesis. The repeat elements and their flanking single copy regions reside either in very long 3\u2032 or 5\u2032-terminal sequences, or in unprocessed intervening sequences in the maternal poly(A) RNA. These findings lead us to the proposal that the majority of the cytoplasmic poly(A) RNA in echinoderm eggs and early embryos is similar in form to RNAs that occur in the nucleus rather than to the messenger RNA of later cells.", "doi": "10.1016/S0022-2836(83)80340-4", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1983-06-25", "series_number": "2", "volume": "167", "issue": "2", "pages": "361-389" }, { "id": "authors:qj3fx-yq208", "collection": "authors", "collection_id": "qj3fx-yq208", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-070445446", "type": "article", "title": "Transcripts of Three Mitochondrial Genes in the RNA of Sea Urchin Eggs and Embryos", "author": [ { "family_name": "Cabrera", "given_name": "Carlos V.", "clpid": "Cabrera-C-V" }, { "family_name": "Jacobs", "given_name": "Howard T.", "clpid": "Jacobs-H-T" }, { "family_name": "Posakony", "given_name": "James W.", "clpid": "Posakony-J-W" }, { "family_name": "Grula", "given_name": "John W.", "clpid": "Grula-J-W" }, { "family_name": "Roberts", "given_name": "John W.", "clpid": "Roberts-J-W" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "cDNA clones representing mitochondrial 16 S rRNA, and mRNAs for cytochrome oxidase I and an unidentified reading frame were used to measure the prevalence and stability of these transcripts in gastrula stage embryos. The 16 S rRNA is the most prevalent embryo poly(A) RNA, and is synthesized about four times more rapidly than is the mRNA for cytochrome oxidase. The relative prevalence of the two mRNAs is largely determined by their turnover rates.", "doi": "10.1016/0012-1606(83)90107-0", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1983-06", "series_number": "2", "volume": "97", "issue": "2", "pages": "500-505" }, { "id": "authors:n32tg-fym91", "collection": "authors", "collection_id": "n32tg-fym91", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160518-090554349", "type": "article", "title": "Mitochondrial DNA Sequences in the Nuclear Genome of Strongylocentrotus purpuratus", "author": [ { "family_name": "Jacobs", "given_name": "Howard T.", "clpid": "Jacobs-H-T" }, { "family_name": "Posakony", "given_name": "James W.", "clpid": "Posakony-J-W" }, { "family_name": "Grula", "given_name": "John W.", "clpid": "Grula-J-W" }, { "family_name": "Roberts", "given_name": "John W.", "clpid": "Roberts-J-W" }, { "family_name": "Xin", "given_name": "Ji-Hou", "clpid": "Xin-Ji-Hou" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Two sea urchin embryo complementary DNA clones representing mitochondrial 16 S ribosomal RNA and cytochrome oxidase subunit I messenger RNA have been characterized. The cloned cDNAs are colinear with sea urchin mitochondrial DNA, and their identification is based on cross-hybridization with known restriction fragments of human mitochondrial DNA, and on nucleotide sequence determinations. The mitochondrial cDNA clones also displayed an unexpected reaction with specific genomic DNA sequences in gel blot hybridizations. Genomic phage \u03bb recombinants containing sequences hybridizing with the mitochondrial clones were isolated and the arrangement of these sequences was determined. The genomic region studied contains a sequence homologous with the 3\u2032 end of the mitochondrial 16 S rRNA gene, flanked on one side by what is possibly a complete copy of the cytochrome oxidase subunit I gene, and on the other by a duplication of a fragment of this gene. The nucleotide sequence divergence between the mitochondrial and nuclear homologues of the cytochrome oxidase subunit I gene varies for different regions of the gene, from about 13% to 25%, while there is about 8% sequence divergence between nuclear and mitochondrial versions of the 3\u2032 16 S rRNA sequence. The structure of the genomic mitochondrial sequence homologues indicates that during sea urchin evolution there occurred a germ-line transposition of a fragment of the mitochondrial genome into the nuclear DNA, followed by rearrangements and single nucleotide substitutions.", "doi": "10.1016/S0022-2836(83)80270-8", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1983-04-23", "series_number": "4", "volume": "165", "issue": "4", "pages": "609-632" }, { "id": "authors:twqep-raf88", "collection": "authors", "collection_id": "twqep-raf88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160517-092307303", "type": "article", "title": "Eukaryotic gene expression: Very short repeats and coordinate induction of genes", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Jacobs", "given_name": "Howard T.", "clpid": "Jacobs-H-T" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The proposition that a set of unlinked\ngenes could be coordinately induced by\nmeans of cis interactions with a common\nregulatory molecule retains an attractive\nsimplicity. The idea requires that some\nform of homologous sequence exists in the\nvicinity of genes that are functionally\nrelated and are induced in concert. As\nprimary sequence data for sets of such\ngenes have become available, several\ninteresting homologies have indeed turned\nup. Though the shared sequence elements\nare quite short, the statistical probability of\ntheir chance occurrence in similar positions\nwith respect to each of the several\ncoordinately induced genes is extremely\nlow. Furthermore, in two such cases, direct\nevidence has been obtained by DNA\ntransformation that the short repeated\nsequence elements shared among the\n5'-flanking regions of the inducible genes\nare required for regulation.", "doi": "10.1038/301468a0", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "1983-02-10", "series_number": "5900", "volume": "301", "issue": "5900", "pages": "468-470" }, { "id": "authors:07kjj-gr121", "collection": "authors", "collection_id": "07kjj-gr121", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151217-181955149", "type": "book_section", "title": "Poly(A) RNA of the Egg Cytoplasm: Structural Resemblance to the Nuclear RNA of Somatic Cells", "book_title": "Molecular Biology of Egg Maturation", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Jacobs", "given_name": "Howard T.", "clpid": "Jacobs-H-T" }, { "family_name": "Thomas", "given_name": "Terry L.", "clpid": "Thomas-T-L" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "contributor": [ { "family_name": "Porter", "given_name": "Ruth", "clpid": "Porter-R" }, { "family_name": "Whelan", "given_name": "Julie", "clpid": "Whelan-J" } ], "abstract": "This paper concerns the structural characteristics of the poly(A) RNA stored in unfertilized amphibian and echinoderm eggs. Though located in the egg cytoplasm, at least two-thirds of these maternal transcripts display an interspersed sequence organization similar to that of nuclear RNA. In Xenopus laevis interspersed poly(A) RNA molecules are synthesized and deposited in the oocyte cytoplasm throughout the main growth phase of oogenesis. Regions of the sea urchin genome that are represented by interspersed maternal transcripts have been recovered from recombinant clone libraries. In one case the same single-copy sequence is found both in an abundant message-sized 1.6 kilobase (kb) maternal transcript and in a 7.5 kb maternal transcript that structurally resembles a precursor form and is not found in embryonic polysomes. In a second example considered, a 9.5 kb transcript was identified in embryo nuclear RNA that may be identical in structure with an interspersed maternal poly(A) RNA derived from the same transcription unit. Transcription of this sequence appears to be constitutive in somatic cell nuclei, though no homologous cytoplasmic RNAs are found after early cleavage. This may be a widespread form of regulation for transcription units expressed in female germ cells, and represented in the maternal poly(A) RNA pools of unfertilized eggs.", "doi": "10.1002/9780470720790.ch2", "isbn": "9780272797303", "publisher": "Wiley", "place_of_publication": "New York, NY", "publication_date": "1983", "pages": "6-24" }, { "id": "authors:12qpf-jyx34", "collection": "authors", "collection_id": "12qpf-jyx34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160413-111516155", "type": "article", "title": "An Interspersed Region of the Sea Urchin Genome Represented in Both Maternal Poly(A) RNA and Embryo Nuclear RNA", "author": [ { "family_name": "Thomas", "given_name": "Terry L.", "clpid": "Thomas-T-L" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The sequence organization and transcriptional expression of a 17-kb region of the Strongylocentrotus purpuratus genome are described in this report. This region includes a transcription unit, designated \"gene 88,\" that is represented by a typical low prevalence maternal poly(A) RNA. The predominant maternal gene 88 transcript is about 9.5 kb in length, and analysis of the sequence organization of the cloned genomic region encoding this transcript shows that it contains a high density of low and moderately prevalent repeat sequences, as well as \u22652 kb of single-copy sequence. Genome blots carried out with DNA from different individual sea urchins show that several allelic forms of this single-copy region exist. The transcribed single-copy sequence is only slightly less polymorphic than is the average single-copy sequence of the S. purpuratus genome. Gene 88 single-copy sequences appear to be represented in at least three smaller transcripts in the polysomal RNA of 16-cell embryos. The nuclear RNA of later embryos also contains gene 88 transcripts. RNA gel blots indicate that polyadenylated gene 88 transcripts are also 9.5 kb in length in blastula and gastrula nuclear RNAs and these transcripts are probably colinear with the major maternal RNA transcript.", "doi": "10.1016/0012-1606(82)90086-0", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1982-11", "series_number": "1", "volume": "94", "issue": "1", "pages": "230-239" }, { "id": "authors:mjmpb-r3p96", "collection": "authors", "collection_id": "mjmpb-r3p96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150204-145027606", "type": "article", "title": "Molecular Biology of the Sea Urchin Embryo", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Research on the early development of the sea urchin offers new insights into the process of embryogenesis. Maternal messenger RNA stored in the unfertilized egg supports most of the protein synthesis in the early embryo, but the structure of maternal transcripts suggests that additional functions are also possible. The overall developmental patterns of transcription and protein synthesis are known, and current measurements describe the expression of specific genes, including the histone genes, the ribosomal genes, and the actin genes. Possible mechanisms of developmental commitment are explored for regions of the early embryo that give rise to specified cell lineages, such as the micromere-mesenchyme cell lineage.", "doi": "10.1126/science.6178156", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1982-07-02", "series_number": "4554", "volume": "217", "issue": "4554", "pages": "17-26" }, { "id": "authors:3x9w2-7wv65", "collection": "authors", "collection_id": "3x9w2-7wv65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170606-071232789", "type": "article", "title": "Sea Urchin DNA Sequence Variation and Reduced Interspecies Differences of the Less Variable DNA Sequences", "author": [ { "family_name": "Grula", "given_name": "J. W.", "clpid": "Grula-J-W" }, { "family_name": "Hall", "given_name": "T. J.", "clpid": "Hall-T-J" }, { "family_name": "Hunt", "given_name": "J. A.", "clpid": "Hunt-J-A" }, { "family_name": "Giugni", "given_name": "T. D.", "clpid": "Giugni-T-D" }, { "family_name": "Graham", "given_name": "G. J.", "clpid": "Graham-G-J" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" } ], "abstract": "Individual sea urchins of the species Stronglyocentrotus purpuratus differ from each other in about 4% of the nucleotide pairs of their single copy DNA sequences (Britten et al., 1978). In the past we have referred to single copy DNA sequence polymorphism (Britten et al., 1978), but for purposes of clarity we use here the term sequence variation which is defined as the percent difference in sequence between individual genomes averaged for a population and averaged over all of the single copy DNA.", "doi": "10.1111/j.1558-5646.1982.tb05434.x", "issn": "0014-3820", "publisher": "Wiley", "publication": "Evolution", "publication_date": "1982-07", "series_number": "4", "volume": "36", "issue": "4", "pages": "665-676" }, { "id": "authors:r044f-6c789", "collection": "authors", "collection_id": "r044f-6c789", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160413-111515543", "type": "article", "title": "Developmental Patterns of Cytoplasmic Transcript Prevalence in Sea Urchin Embryos", "author": [ { "family_name": "Flytzanis", "given_name": "Constantin N.", "clpid": "Flytzanis-C-N" }, { "family_name": "Brandhorst", "given_name": "Bruce P.", "clpid": "Brandhorst-B-P" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Several hundred two-cell stage, gastrula stage, and pluteus stage sea urchin embryo cDNA clones were screened with [^(32)P]cDNA transcribed from a developmental series of cytoplasmic and polysomal poly(A) RNAs. Transcript prevalence was estimated by reference to the reaction of a series of standard clones complementary to RNAs of known abundance. We describe the dominant pattern of prevalence change during development for abundant sequences, i.e., those present in the range 5 \u00d7 10^4\u201310^6 molecules/embryo. These transcripts are most often about equally abundant in egg and pluteus stage embryos, and are severalfold less prevalent at gastrula stage. Less than 10% of the sequences displaying this pattern undergo >10-fold changes in prevalence during development. A search for later embryo sequences not represented detectably in egg or cleavage stage embryo poly(A) RNA yielded a number of examples. These were confirmed by the RNA gel blot method. Sequences regulated in this manner all belonged to lower abundance classes, and are present at about 40 copies/cell or less at the gastrula stage.", "doi": "10.1016/0012-1606(82)90004-5", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1982-05", "series_number": "1", "volume": "91", "issue": "1", "pages": "27-35" }, { "id": "authors:2fmkh-qx334", "collection": "authors", "collection_id": "2fmkh-qx334", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-144015317", "type": "article", "title": "Sequence Organization of the Poly(A) RNA Synthesized and Accumulated in Lampbrush Chromosome Stage Xenopus laevis Oocytes", "author": [ { "family_name": "Anderson", "given_name": "David M.", "clpid": "Anderson-D-M" }, { "family_name": "Richter", "given_name": "Joel D.", "clpid": "Richter-J-D" }, { "family_name": "Chamberlin", "given_name": "Margaret E.", "clpid": "Chamberlin-M-E" }, { "family_name": "Price", "given_name": "David H.", "clpid": "Price-D-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Smith", "given_name": "L. Dennis", "clpid": "Smith-L-D" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The poly(A) RNA of Xenopus laevis oocytes was extracted, renatured and spread for electron microscopy. As reported for the poly(A) RNA of sea urchin eggs (Costantini et al., 1980), the Xenopus oocyte RNA renatures extensively, revealing the presence of complementary, interspersed repetitive sequences on different RNA molecules. About 68% of the mass of the poly(A) RNA in late ovarian oocytes is included in multimolecular structures after renaturation, and a similar fraction of the poly(A) RNA of mid-lampbrush stage oocytes also contains interspersed repeat sequences. In contrast, less than 15% of the poly(A) RNA molecules of stage 41 tadpoles retains the capacity for RNA duplex formation under the same conditions. Poly(A) RNAs displaying interspersed sequence organization are located in the oocyte cytoplasm. This was shown using manually enucleated oocytes. Lampbrush stage oocytes were injected with [3H]GTP, allowed to incorporate for 48 hours, enucleated, and the poly(A) [3H]RNA extracted. The fraction of the labelled poly(A) RNA that could be attributed to mitochondrial transcription was \u2264 16%, according to measurements made with cloned mitochondrial DNA. By use of a cellulose column that separates RNA-containing duplex regions, the labelled RNA was shown to anneal almost completely with the poly(A) RNA already accumulated in the cytoplasm of the oocytes. The newly synthesized poly(A) RNA exported from lampbrush chromosome stage oocyte nuclei also displays an interspersed sequence organization. RNA synthesized in vitro in isolated germinal vesicles was reacted with six cloned complementary DNAs that contain maternal poly(A) RNA sequences, and all of these probes were represented in the transcription products. Thus the amphibian lampbrush chromosome stage oocyte nucleus synthesizes and transports to the cytoplasm poly(A) RNAs that, are similar in structure and sequence content to the maternal poly(A) RNA stored in the oocyte at the termination of oogenesis. We conclude that this poly(A) RXA turns over slowly, thereby maintaining an approximately constant steady state throughout oogenesis. However, the maternal poly(A) RNA pool is so large that the rate of synthesis required for this process demands the intense and widespread level of transcription observed in lampbrush chromosomes.", "doi": "10.1016/0022-2836(82)90006-7", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1982-03-05", "series_number": "3", "volume": "155", "issue": "3", "pages": "281-309" }, { "id": "authors:fgrzq-k3m97", "collection": "authors", "collection_id": "fgrzq-k3m97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-073658938", "type": "article", "title": "Cloned Embryo mRNAs Not Detectably Expressed in Adult Sea Urchin Coelomocytes", "author": [ { "family_name": "Xin", "given_name": "Ji-Hou", "clpid": "Xin-Ji-Hou" }, { "family_name": "Brandhorst", "given_name": "Bruce P.", "clpid": "Brandhorst-B-P" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A set of 455 cloned pluteus cDNAs was analyzed by colony hybridization to radioactive cDNAs transcribed from cytoplasmic poly(A) RNA of pluteus embryos and adult coelomocytes. The prevalence of transcripts corresponding to each of the clones was estimated by use of cloned standards having known transcript prevalences. While 46% of the clones correspond to transcripts present at more than 105 copies/ng poly(A) RNA (about 5 copies/cell) in plutei, only 5.5% are that prevalent in the coelomocyte. The most prevalent pluteus transcripts are frequently also prevalent in coelomocytes, but more than 85% of the moderately prevalent pluteus transcripts are below the limit of detection of about 1 copy/cell in coelomocytes. None of the clones corresponding to rare transcripts in the pluteus is represented by prevalent transcripts in coelomocytes. The data suggest that the expression of the majority of genes giving rise to moderately prevalent messenger RNAs in embryos must be regulated during the life cycle of the sea urchin, while some very prevalent transcripts may be ubiquitous.", "doi": "10.1016/0012-1606(82)90342-6", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1982-02", "series_number": "2", "volume": "89", "issue": "2", "pages": "527-531" }, { "id": "authors:zwqxd-45y68", "collection": "authors", "collection_id": "zwqxd-45y68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201005-143650069", "type": "book_section", "title": "Genomic Change and Morphological Evolution Group Report", "book_title": "Evolution and Development", "author": [ { "family_name": "Dawid", "given_name": "I.", "clpid": "Dawid-I" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" }, { "family_name": "Dover", "given_name": "G. A.", "clpid": "Dover-G-A" }, { "family_name": "Gallwitz", "given_name": "D. F.", "clpid": "Gallwitz-D-F" }, { "family_name": "Garcia-Bellido", "given_name": "A.", "clpid": "Garcia-Bellido-A" }, { "family_name": "Kafatos", "given_name": "F. C.", "clpid": "Kafatos-F-C" }, { "family_name": "Kauffman", "given_name": "S. A.", "clpid": "Kauffman-S-A" }, { "family_name": "Moritz", "given_name": "K.", "clpid": "Moritz-K" }, { "family_name": "Ohno", "given_name": "S.", "clpid": "Ohno-S" }, { "family_name": "Schmidtke", "given_name": "J.", "clpid": "Schmidtke-J" }, { "family_name": "Sch\u00fctz", "given_name": "G.", "clpid": "Sch\u00fctz-G" } ], "contributor": [ { "family_name": "Bonner", "given_name": "J. T.", "clpid": "Bonner-J-T" } ], "abstract": "In our discussions, questions of gene and chromosome organization and possible functional correlates of this organization were treated, as were sequence and organizational changes observed in evolution. We further considered existing knowledge and interpretations regarding the actions of genes in development, how genes are utilized, why so many are needed, and how their arrangement may affect activity. We discussed gene famlies, repeated sequences, and in particular, transposable DNA elements and the consequences of their existence for genomic flexibility. Specifically genetic approaches to the study of gene function were addressed, leading to the discussion of gene hierarchies and the apparent existence of control genes. Finally, we considered the problems posed by the activity of many genes and the probable existence of very large numbers of interactions between them.", "doi": "10.1007/978-3-642-45532-2_2", "isbn": "9783642455346", "publisher": "Springer Berlin Heidelberg", "place_of_publication": "Berlin", "publication_date": "1982", "pages": "18-39" }, { "id": "authors:edjyb-x6m18", "collection": "authors", "collection_id": "edjyb-x6m18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201001-145812635", "type": "book_section", "title": "Genomic Alterations in Evolution", "book_title": "Evolution and Development", "author": [ { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" } ], "contributor": [ { "family_name": "Bonner", "given_name": "J. T.", "clpid": "Bonner-J-T" } ], "abstract": "To understand the evolution of species it appears that we will need to know the principal sources and kinds of genomic variation and the mechanisms or systems through which genomic variation affects genes, their expression and the phenotype. In addition we will need to know the nature of the populations that give rise to new species and the way in which the selective forces act through the behavior and death of individuals. What we cannot guess at this time is how much more we will also need to learn about the genome and as yet unexpected processes.", "doi": "10.1007/978-3-642-45532-2_3", "isbn": "9783642455346", "publisher": "Springer Berlin Heidelberg", "place_of_publication": "Berlin, Heidelberg", "publication_date": "1982", "pages": "41-64" }, { "id": "authors:4k6y7-cmh31", "collection": "authors", "collection_id": "4k6y7-cmh31", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151217-180941519", "type": "article", "title": "Molecular structure of maternal RNA", "author": [ { "family_name": "Thomas", "given_name": "Terry L.", "clpid": "Thomas-T-L" }, { "family_name": "Posakony", "given_name": "James W.", "clpid": "Posakony-J-W" }, { "family_name": "Anderson", "given_name": "David M.", "clpid": "Anderson-D-M" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The presence of a stable maternal mRNA population in mature oocytes of many species is well established. In this paper we show that the mature egg contains, in addition to these mature mRNAs, a structurally more complex population of RNA transcripts. This latter class of RNA consists of polyadenylated transcripts of repetitive and nonrepetitive DNA elements covalently linked into long interspersed molecules. As much as seventy percent of the polyadenylated egg RNA of Xenopus laevis and Strongylocentrotus purpuratus is represented in this interspersed population. Most of the nonrepetitive DNA sequences represented in the mature mRNA population are also present in the interspersed RNA. These transcripts have an organization similar to that of somatic cell nuclear RNA. Data are presented that suggests some of these interspersed maternal transcripts are unprocessed precursor-like molecules. Some possible functions of this novel class of RNA during early development are discussed.", "doi": "10.1007/BF00286022", "issn": "0009-5915", "publisher": "Springer", "publication": "Chromosoma", "publication_date": "1981-12", "series_number": "3", "volume": "84", "issue": "3", "pages": "319-335" }, { "id": "authors:pwth5-57h34", "collection": "authors", "collection_id": "pwth5-57h34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151224-073924180", "type": "article", "title": "Evolutionary distances in hawaiian drosophila measured by DNA reassociation", "author": [ { "family_name": "Hunt", "given_name": "John A.", "clpid": "Hunt-J-A" }, { "family_name": "Hall", "given_name": "Terrence J.", "clpid": "Hall-T-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Comparisons of the sequence divergence of three species of Hawaiian Drosophila have been made by hybridization of single-copy tracer DNA of each of the species with driver DNA from each species, and measurement of the average melting temperature (Tma) in a chaotropic solvent (2.4 M tetraethylammonium chloride) which minimizes differences due to base composition. Correction was made for the length of hybrid duplex regions to obtain the reduction in thermal stability due to divergence. \n\nAn accuracy of \u00b1 0.2\u00b0C was achieved and the mean reduction in Tm for hybridization betweenD. heteroneura andD. silvestris (found only on the island of Hawaii) was 0.55\u00b0C and betweenD. picticornis, found only on the island of Kauai, and the other two species was 2.13\u00b0C. The rate of DNA change is estimated to be between 0.2 and 0.4%/My by assuming that theD. heteroneura-D. silvestris divergence occurred 0.8 My ago and the divergence between these species andD. picticornis between 4 and 6 My ago. \n\nThe general single copy DNA sequence divergence appears to be very much greater than the minimal coding region sequence divergence previously estimated from allozyme studies.", "doi": "10.1007/BF01734358", "issn": "0022-2844", "publisher": "Springer Verlag", "publication": "Journal of Molecular Evolution", "publication_date": "1981-11", "series_number": "6", "volume": "17", "issue": "6", "pages": "361-367" }, { "id": "authors:08ks7-71f13", "collection": "authors", "collection_id": "08ks7-71f13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160520-115157049", "type": "article", "title": "Long and short repeats of sea urchin DNA and their evolution", "author": [ { "family_name": "Moore", "given_name": "Gordon P.", "clpid": "Moore-G-P" }, { "family_name": "Pearson", "given_name": "William R.", "clpid": "Pearson-W-R" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Repeated sequences cloned from the DNA of the sea urchin S. purpuratus were used as probes to measure the lengths of individual families of repeats. Some probes reassociated much more rapidly with preparations of long repeats than with short repeats while others reassociated more rapidly with short repeats than with long repeats. In this way two of five cloned repeats were shown to represent families with a great majority of sequences in the long class. One represented a family with similar numbers of long and short class members. Two were members of predominantly short class families. \u2014 The cloned repeats representing long class families, formed more precise duplexes than those representing short class families. Thermal stability measurements using S. purpuratus or S. franciscanus driver DNA showed that precise repetitive sequences have as great an interspecies sequence difference as the less precise repeats. Thus the precision of many families may result from recent multiplication rather than from selective pressure on the DNA sequences. Measurements of evolutionary frequency change show a clear correlation between the frequency change and the size of families of repeats in S. purpuratus. Comparison with S. franciscanus indicates that many of the large size families in S. purpuratus are those that have grown in size since these two species diverged.", "doi": "10.1007/BF00293360", "issn": "0009-5915", "publisher": "Springer", "publication": "Chromosoma", "publication_date": "1981-09", "series_number": "1", "volume": "84", "issue": "1", "pages": "19-32" }, { "id": "authors:8gk9g-7p325", "collection": "authors", "collection_id": "8gk9g-7p325", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SCHEmcb81", "type": "article", "title": "Organization and expression of multiple actin genes in the sea urchin", "author": [ { "family_name": "Scheller", "given_name": "Richard H.", "clpid": "Scheller-R-H" }, { "family_name": "McAllister", "given_name": "Linda B.", "clpid": "McAllister-L-B" }, { "family_name": "Crain", "given_name": "William R., Jr.", "clpid": "Crain-W-R-Jr" }, { "family_name": "Durica", "given_name": "David S.", "clpid": "Durica-D-S" }, { "family_name": "Posakony", "given_name": "James W.", "clpid": "Posakony-J-W" }, { "family_name": "Thomas", "given_name": "Terry L.", "clpid": "Thomas-T-L" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A set of at least 11 actin genes has been isolated from genomic recombinant deoxyribonucleic acid libraries of the sea urchin Strongylocentrotus purpuratus. Most of the isolates derive from a library which represents the genome of a single animal. There are at least five distinct types of sea urchin actin gene, some of which are represented by multiple copies in the genome. The actin gene types are distinguished by nonhomologous flanking sequences and intervening sequences, though the protein coding sequences appear in most cases to be quite similar. Eight of the 11 genes isolated have been recovered in lambda recombinants that contain two actin genes, linked at 5- to 9-kilobase distances. Restriction map overlaps suggest that the genome contains an array of at least three of these genes spaced over about 30 kilobases of deoxyribonucleic acid. In the linkage patterns observed, actin genes of diverse types were linked to each other. In early embryos, actin messenger ribonucleic acid (RNA) transcripts of 1.8 and 2.2 kilobases were found, and the longer of these transcripts was more prevalent in the maternal RNA of the egg. From RNA gel blot experiments, we conclude that the two transcripts derive from different actin gene types. Different repetitive sequences were located to either side of most of the actin genes, and in most observed cases the repeat sequences which were adjacent to actin genes of a given type were similar. The repeat sequences flanking the actin genes belonged to families which were transcribed, but those repeats in the neighborhood of the actin genes which have been investigated were not themselves represented in the stable RNAs of eggs or early embryos.", "pmcid": "PMC369709", "issn": "0270-7306", "publisher": "American Society for Microbiology", "publication": "Molecular and Cellular Biology", "publication_date": "1981-07", "series_number": "7", "volume": "1", "issue": "7", "pages": "609-628" }, { "id": "authors:669tp-wr911", "collection": "authors", "collection_id": "669tp-wr911", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160415-074134645", "type": "article", "title": "Repetitive Sequences of the Sea Urchin Genome II. Subfamily Structure and Evolutionary Conservation", "author": [ { "family_name": "Scheller", "given_name": "Richard H.", "clpid": "Scheller-R-H" }, { "family_name": "Anderson", "given_name": "David M.", "clpid": "Anderson-D-M" }, { "family_name": "Posakony", "given_name": "James W.", "clpid": "Posakony-J-W" }, { "family_name": "McAllister", "given_name": "Linda B.", "clpid": "McAllister-L-B" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Members of three repetitive sequence families were isolated from recombinant \u03bb-genome libraries, and were used to investigate sequence relationships within these families. Studies presented elsewhere show that members of all three repeat sequence families are transcribed tissue-specifically. The thermal stability of intrafamilial heteroduplexes was measured, and the extent of colinearity between related sequences was determined by restriction mapping, heteroduplex visualization, gel blot hybridization, and direct sequencing. One large and very divergent family, named 2108, was shown to consist of an assemblage of many small repeat sequence subfamilies. Each subfamily includes <40 members which are not contiguous in the genome but are very closely related colinear sequence elements several thousand nucleotides in length. The different 2108 subfamilies share only small sequence subelements, which in each subfamily occur in a different linear order and are surrounded by different sequences. A second divergent family consisting of short repetitive sequences, the 2109 family, includes many small internally homologous subfamilies as well. A third family, 2034, displays little internal sequence divergence and no apparent subfamily structure. The repeat sequence subfamilies may be biologically significant units of repetition. Thus specific 2108 subfamilies were shown to be evolutionary conserved to a remarkable degree. Highly homologous 2108 sequences were found shared among sea urchin species which diverged almost 200 million years ago, although only about 10% of the single copy DNA sequences of these species are now homologous enough to crossreact.", "doi": "10.1016/0022-2836(81)90258-8", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1981-06-15", "series_number": "1", "volume": "149", "issue": "1", "pages": "15-39" }, { "id": "authors:h6bj6-w7z68", "collection": "authors", "collection_id": "h6bj6-w7z68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160413-091052014", "type": "article", "title": "Repetitive Sequences of the Sea Urchin Genome III. Nucleotide Sequences of Cloned Repeat Elements", "author": [ { "family_name": "Posakony", "given_name": "J. W.", "clpid": "Posakony-J-W" }, { "family_name": "Scheller", "given_name": "R. H.", "clpid": "Scheller-R-H" }, { "family_name": "Anderson", "given_name": "D. M.", "clpid": "Anderson-D-M" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" } ], "abstract": "The nucleotide sequences of eight randomly selected, cloned, repetitive sequence elements were determined. No homologies exist among the eight sequences that are sufficient to promote cross-reaction between them under standard conditions of measurement. Thus, each sequence is representative of a different repeat sequence family. Statistically significant but short (8 to 41 nucleotides) internal direct and inverse repetitions occupy a minor fraction of the sequence length in five of the eight repeat sequences. None contains internal reverse repeats sufficiently long to permit inclusion in the \"foldback\" DNA fraction. The general lack of internal sequence homology means that the sequence complexity of the eight clones is approximately equal to the length of the cloned inserts. Nucleotide sequences of three different members of one particular short interspersed repeat sequence family are also reported. Comparison of these sequences reveals that both the number and order of internal sequence subelements differ among family members. The results show that both fine-scale rearrangement and sequence divergence have occurred during the evolution of this repeat family.", "doi": "10.1016/0022-2836(81)90259-X", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1981-06-15", "series_number": "1", "volume": "149", "issue": "1", "pages": "41-67" }, { "id": "authors:ezt1w-1sk14", "collection": "authors", "collection_id": "ezt1w-1sk14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160415-075415327", "type": "article", "title": "Repetitive Sequences of the Sea Urchin Genome Distribution of Members of Specific Repetitive Families", "author": [ { "family_name": "Anderson", "given_name": "David M.", "clpid": "Anderson-D-M" }, { "family_name": "Scheller", "given_name": "Richard H.", "clpid": "Scheller-R-H" }, { "family_name": "Posakony", "given_name": "James W.", "clpid": "Posakony-J-W" }, { "family_name": "McAllister", "given_name": "Linda B.", "clpid": "McAllister-L-B" }, { "family_name": "Trabert", "given_name": "Steven G.", "clpid": "Trabert-S-G" }, { "family_name": "Beall", "given_name": "Clifford", "clpid": "Beall-C" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Three repetitive sequence families from the sea urchin genome were studied, each defined by homology with a specific cloned probe one to a few hundred nucleotides long. Recombinant \u03bb-sea urchin DNA libraries were screened with these probes, and individual recombinants were selected that include genomic members of these families. Restriction mapping, gel blot, and kinetic analyses were carried out to determine the organization of each repeat family. Sequence elements belonging to the first of the three repeat families were found to be embedded in longer repeat sequences. These repeat sequences frequently occur in small clusters. Members of the second repeat family are also found in a long repetitive sequence environment, but these repeats usually occur singly in any given region of the DNA. The sequences of the third repeat are only 200 to 300 nucleotides long, and are generally terminated by single copy DNA, though a few examples were found associated with other repeats. These three repeat sequence families constitute sets of homologous sequence elements that relate distant regions of the DNA.", "doi": "10.1016/0022-2836(81)90332-6", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1981-01-05", "series_number": "1", "volume": "145", "issue": "1", "pages": "5-28" }, { "id": "authors:9m6m5-e3a43", "collection": "authors", "collection_id": "9m6m5-e3a43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160518-083158924", "type": "article", "title": "Message sequences and short repetitive sequences are interspersed in sea urchin egg poly(A)^+ RNAs", "author": [ { "family_name": "Costantini", "given_name": "Franklin D.", "clpid": "Costantini-F-D" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "At least half of the mass and most of the different single-copy maternal mRNA sequences in the egg are covalently associated with transcripts of short repetitive sequences. Only a restricted group of the diverse genomic repeat families are significantly represented. The messages fall into several hundred sets, each containing transcripts from a different repeat family.", "doi": "10.1038/287111a0", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "1980-09-11", "series_number": "5778", "volume": "287", "issue": "5778", "pages": "111-117" }, { "id": "authors:jgqac-v0190", "collection": "authors", "collection_id": "jgqac-v0190", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160413-091053190", "type": "article", "title": "Limited Complexity of the RNA in Micromeres of Sixteen-Cell Sea Urchin Embryos", "author": [ { "family_name": "Ernst", "given_name": "Susan G.", "clpid": "Ernst-S-G" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The sequence complexity of sea urchin embryo micromere RNA is about 75% of that of total 16-cell embryo cytoplasmic RNA, as reported earlier by Rodgers and Gross [Rodgers, W. H., and Gross, P. R. (1978) Cell, 14, 279\u2013288]. In contrast to the rest of the embryo, there are few, if any, complex maternal RNA species in the micromere cytoplasm which are not represented in the polysomes. The micromeres do not contain detectable quantities of high-complexity nuclear RNA, though such RNA exists in other cells of the fourth-cleavage embryo.", "doi": "10.1016/0012-1606(80)90077-9", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1980-09", "series_number": "1", "volume": "79", "issue": "1", "pages": "119-127" }, { "id": "authors:372k0-7em31", "collection": "authors", "collection_id": "372k0-7em31", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:LASpnas80", "type": "article", "title": "Messenger RNA prevalence in sea urchin embryos measured with cloned cDNAs", "author": [ { "family_name": "Lasky", "given_name": "Laurence A.", "clpid": "Lasky-L-A" }, { "family_name": "Lev", "given_name": "Ze'ev", "clpid": "Lev-Z" }, { "family_name": "Xin", "given_name": "Ji-Hou", "clpid": "Xin-Ji-Hou" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "mRNA prevalence during sea urchin development was measured by treating cDNA clone colonies with labeled cDNAs transcribed from unfertilized egg and embryo poly(A)-RNAs. The number of cytoplasmic transcripts per embryo complementary to several clones was determined independently by titration with poly(A)-RNA in solution, and the amount of cDNA bound to these clones in colony hybridizations was shown to be proportional to the concentration of the respective poly(A)-RNAs in the embryo cytoplasm. At the gastrula stage, the most prevalent mRNA species occur in about 106 molecules per embryo. If all cells were equivalent, this would be a few hundred molecules per cell. By pluteus stage, the prevalence of some sequences has increased more than 10-fold. Most, though not all, sequences prevalent in later embryos are also present in the maternal RNA of the unfertilized egg. For most poly(A)-RNA sequences, the prevalence levels determined during oogenesis are maintained through the pluteus stage, whereas a minority of sequences display sharp stage-specific changes in representation during development.", "pmcid": "PMC350049", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1980-09", "series_number": "9", "volume": "77", "issue": "9", "pages": "5317-5321" }, { "id": "authors:zwhx1-h6s10", "collection": "authors", "collection_id": "zwhx1-h6s10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:LEEpnas80", "type": "article", "title": "Four sizes of transcript produced by a single sea urchin gene expressed in early embryos", "author": [ { "family_name": "Lee", "given_name": "Amy Shiu", "clpid": "Lee-A-S" }, { "family_name": "Thomas", "given_name": "Terry L.", "clpid": "Thomas-T-L" }, { "family_name": "Lev", "given_name": "Ze'ev", "clpid": "Lev-Z" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "This report concerns a set of sea urchin egg and embryo transcripts complementary to a single-copy region of a cloned DNA fragment (Sp88). Three distinct 16-cell embryo polysomal RNA species were found to hybridize with this fragment. These RNAs are about 1700, 3000, and 4000 nucleotides (nt) in length, and the same species were identified in unfertilized eggs. A significant fraction of all three species of the egg and early embryo transcripts is polyadenylylated. At gastrula stage Sp88 transcripts are almost completely confined to the nucleus [Lev, Z., Thomas, T. L., Lee, A. S., Angerer, R. C., Britten, R. J. & Davidson, E. H. (1980) Dev. Biol. 75, in press]. The Sp88 transcripts of gastrulae are present as a fourth RNA species approximately 5800 nt in length. The four species share a sequence element of the cloned DNA fragment that is about 1000 nt long. These RNAs constitute a set of alternative partially overlapping transcripts from the same genomic region.", "pmcid": "PMC349594", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1980-06", "series_number": "6", "volume": "77", "issue": "6", "pages": "3259-3263" }, { "id": "authors:b38p5-3y697", "collection": "authors", "collection_id": "b38p5-3y697", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151217-180729734", "type": "article", "title": "Evolution of sea urchin non-repetitive DNA", "author": [ { "family_name": "Hall", "given_name": "Terrence J.", "clpid": "Hall-T-J" }, { "family_name": "Grula", "given_name": "John W.", "clpid": "Grula-J-W" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "New methods have been applied to the determination of single copy DNA sequence differences between the sea urchin species Strongylocentrotus purpuratus, S. franciscanus, S. drobachiensis, and Lytechinus pictus. The thermal stability of interspecies DNA duplexes was measured in a solvent (2.4 M tetraethylammonium chloride) that suppresses the effect of base composition on melting temperature. The lengths of duplexes were measured after digestion with S1 nuclease and correction made for the effect of length on thermal stability. The degree of base substitution that has occurred in the single copy DNA during sea urchin evolution is significantly larger than indicated by earlier measurements. We estimate that 19% of the nucleotides of the single copy DNA are different in the genomes of the two sea urchin congeners, S. purpuratus, and S. franciscanus, which apparently diverged only 15 to 20 million years ago.", "doi": "10.1007/BF01731580", "issn": "0022-2844", "publisher": "Springer Verlag", "publication": "Journal of Molecular Evolution", "publication_date": "1980-06", "series_number": "2", "volume": "16", "issue": "2", "pages": "95-110" }, { "id": "authors:9kjjy-39r48", "collection": "authors", "collection_id": "9kjjy-39r48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150128-094603323", "type": "article", "title": "Evolutionary Conservation of Repetitive Sequence Expression in Sea Urchin Egg RNA's", "author": [ { "family_name": "Moore", "given_name": "Gordon P.", "clpid": "Moore-G-P" }, { "family_name": "Costantini", "given_name": "Franklin D.", "clpid": "Costantini-F-D" }, { "family_name": "Posakony", "given_name": "James W.", "clpid": "Posakony-J-W" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Cloned repetitive DNA sequences were used to determine the number of homologous RNA transcripts in the eggs of two sea urchin species, Strongylocentrotus purpuratus and S. franciscanus. The eggs of these species contain different\namounts of RNA, and their genomes contain different numbers of copies of the cloned repeats. The specific pattern of repetitive sequence representation in the two egg RNA' s is nonetheless quantitatively similar. The evolutionary conservation of this pattern suggests the functional importance of repeat sequence expression.", "doi": "10.1126/science.6154974", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1980-05-30", "series_number": "4447", "volume": "208", "issue": "4447", "pages": "1046-1048" }, { "id": "authors:n87xk-z0567", "collection": "authors", "collection_id": "n87xk-z0567", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160517-110120234", "type": "article", "title": "Complexity of RNA in Eggs of Drosophila Melanogaster and Musca Domestica", "author": [ { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Jacobs-Lorena", "given_name": "Marcelo", "clpid": "Jacobs-Lorena-M" }, { "family_name": "Cummings", "given_name": "Michael R.", "clpid": "Cummings-M-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Comparative measurements are presented of the sequence complexity of the RNA stored in the eggs of two dipteran flies, Musca domestica and Drosophila melanogaster. The genome of Musca is about five times the size of the Drosophila genome and contains about 3.6 times as much single-copy sequence. As shown earlier, the interspersion of repetitive and single-copy sequence is of the short-period form in Musca, and is of the long-period form in Drosophila. The egg RNA complexities were determined by hybridization of excess RNA with radioactively labeled single-copy DNA. Complexity is expressed as the length (in nucleotides) of diverse single-copy sequence represented in the RNA. The complexity of the RNA of the Musca egg is about 2.4 x 10^7 nucleotides, and that of the Drosophila egg is about 1.2 x 10^7 nucleotides. The RNA of the Musca egg is similar to or very slightly lower in complexity than that of other egg RNAs, e.g., those of Xenopus and sea urchin. Compared to all previously measured egg RNAs, Drosophila egg RNA is low in sequence complexity.", "pmcid": "PMC1214223", "issn": "0016-6731", "publisher": "Genetics Society of America", "publication": "Genetics", "publication_date": "1980-05-01", "series_number": "1", "volume": "95", "issue": "1", "pages": "81-94" }, { "id": "authors:f99x2-qgr22", "collection": "authors", "collection_id": "f99x2-qgr22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160413-091052613", "type": "article", "title": "Developmental Expression of Two Cloned Sequences Coding for Rare Sea Urchin Embryo Messages", "author": [ { "family_name": "Lev", "given_name": "Ze'ev", "clpid": "Lev-Z" }, { "family_name": "Thomas", "given_name": "Terry L.", "clpid": "Thomas-T-L" }, { "family_name": "Lee", "given_name": "Amy S.", "clpid": "Lee-A-S" }, { "family_name": "Angerer", "given_name": "Robert C.", "clpid": "Angerer-R-C" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Measurements are presented of the number of transcripts in sea urchin embryos and in adult intestine cells complementary to two cloned genomic single copy sequences. These sequences apparently code for maternal mRNAs stored in the egg. About 1000 and 1400 transcripts are stored per egg, close to the average value for maternal mRNAs. RNAs complementary to the cloned sequences are also found in the polysomal message of early embryos. The number of polysomal transcripts representing each cloned sequence is typical of the \"complex\" or \"rare\" class of message in sea urchin embryos. Expression of these putative complex class structural genes is regulated developmentally. Thus, polysomal transcripts of both sequences essentially disappear by the blastula stage. One sequence is again represented at a low level in adult intestine cytoplasmic RNA while the other is absent. However, in all the developmental stages examined, the number of nuclear transcripts of the cloned sequences remains about the same as for any average single copy sequence transcript.", "doi": "10.1016/0012-1606(80)90382-6", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1980-05", "series_number": "2", "volume": "76", "issue": "2", "pages": "322-340" }, { "id": "authors:xr1yn-5kf92", "collection": "authors", "collection_id": "xr1yn-5kf92", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160413-111515793", "type": "article", "title": "Complexity of RNA in developing oocytes of Drosophila melanogaster", "author": [ { "family_name": "Jacobs-Lorena", "given_name": "M.", "clpid": "Jacobs-Lorena-M" }, { "family_name": "Hough-Evans", "given_name": "B. R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" } ], "abstract": "RNA was extracted from Drosophila egg chambers which had been separated into four size classes, and in addition from mature ovarian eggs. The RNAs were hybridized with a Drosophila single-copy DNA tracer. Egg chamber RNAs from all stages of oogenesis examined contained single-copy DNA transcripts equal in complexity to the RNA of the mature egg.", "doi": "10.1016/0012-1606(80)90399-1", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1980-05", "series_number": "2", "volume": "76", "issue": "2", "pages": "509-513" }, { "id": "authors:xakzg-6r798", "collection": "authors", "collection_id": "xakzg-6r798", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150729-112354343", "type": "article", "title": "Regulation of gene expression: possible role of repetitive sequences", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Large contrasts are observed between the messenger RNA populations of different tissues and of embryos at different stages of development. Nevertheless, coding sequences for genes not expressed in a cell appear to be present in its nuclear RNA. Though many nuclear RNA transcripts of single copy DNA sequences are held in common between tissues, an additional set, probably consisting of non-message sequences, is not shared. Nuclear RNA also contains transcripts of repetitive DNA sequences. Certain repeat families are represented at high levels in the nuclear RNA of particular tissues and much lower levels in others. It is surprising that both complements of most repeat sequences are present in nuclear RNA. These observations lead to model for regulation of gene expression in which the formation of repetitive RNA-RNA duplexes controls the production of messenger RNA.", "doi": "10.1126/science.451548", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1979-06-08", "series_number": "4397", "volume": "204", "issue": "4397", "pages": "1052-1059" }, { "id": "authors:v4zcc-hha93", "collection": "authors", "collection_id": "v4zcc-hha93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ERNpnas79", "type": "article", "title": "Distinct Single-Copy Sequence Sets in Sea Urchin Nuclear RNAs", "author": [ { "family_name": "Ernst", "given_name": "Susan G.", "clpid": "Ernst-S-G" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The purpose of this study was to determine whether nuclear RNAs (nRNA) of sea urchin embryos and adult tissues contain identical or partially distinct sets of single-copy sequence transcripts. A DNA tracer was prepared consisting mainly of sequences absent from gastrula nRNA; 3.6% of this tracer reacted with adult intestine nRNA but not with gastrula nRNA. The existence of a differentially transcribed DNA fraction was verified by its partial purification and rehybridization to intestine and gastrula nRNAs. About one-third of the genomic single-copy sequence is represented in both nRNAs, or about 2 x 10^8 nucleotides. The differentially transcribed portion of the single-copy genome identified in this work includes about 3.5 x 10^7 nucleotides.", "pmcid": "PMC383567", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1979-05", "series_number": "5", "volume": "76", "issue": "5", "pages": "2209-2212" }, { "id": "authors:n06yh-a7756", "collection": "authors", "collection_id": "n06yh-a7756", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-123231702", "type": "article", "title": "RNA complexity in developing sea urchin oocytes", "author": [ { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Ernst", "given_name": "Susan G.", "clpid": "Ernst-S-G" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Nuclear and cytoplasmic RNAs extracted from previtellogenic and vitellogenic oocytes of the sea urchin Strongylocentrotus purpuratus were characterized by hybridization reactions with radioactively labeled single-copy sea urchin DNA. The complexity of nuclear RNA from previtellogenic oocytes was 1.6 \u00d7 10^8 nucleotides. The previtellogenic nuclear RNA sequence set is included in the hnRNA of gastrula stage embryos. The nulcear RNA of vitellogenic oocytes may also contain a class of more prevalent transcripts. A single-copy [^3H]DNA tracer enriched for the sequences of mature egg RNA was reacted with cytoplasmic RNA of previtellogenic oocytes. This experiment showed that less than half of the mature egg RNA sequence set is accumulated before the onset of vitellogenesis. Therefore, a large fraction of the maternal message sequences appears in the egg during the last several weeks of oocyte development.", "doi": "10.1016/0012-1606(79)90290-2", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1979-03", "series_number": "1", "volume": "69", "issue": "1", "pages": "258-269" }, { "id": "authors:znbmb-x6h31", "collection": "authors", "collection_id": "znbmb-x6h31", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-124303715", "type": "article", "title": "The single-copy DNA sequence polymorphism of the sea urchin strongylocentrotus purpuratus", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Cetta", "given_name": "Anita", "clpid": "Cetta-A" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The single-copy DNA sequence difference between individual sea urchins of the species Strongylocentrotus purpuratus has been estimated by comparing the thermal stability of reassociated DNA duplexes from two individuals with that for DNA from an individual. Thermal stability was measured by hydroxyapatite thermal chromatography, S1 nuclease resistance after heating in a solvent which neutralizes the effect of DNA base composition, and spectrophotometric melting. One pair of individuals appear to differ from each other in about 4% of the nucleotide pairs of their single-copy DNA sequence. The differences in DNA sequence among individuals in local populations are not distinguishably smaller than those among populations as far apart as 2000 kilometers along the Pacific coast of North America.", "doi": "10.1016/0092-8674(78)90044-2", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1978-12", "series_number": "4", "volume": "15", "issue": "4", "pages": "1175-1186" }, { "id": "authors:taj6g-t0a80", "collection": "authors", "collection_id": "taj6g-t0a80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-125227868", "type": "article", "title": "Evolutionary change in the repetition frequency of sea urchin DNA sequences", "author": [ { "family_name": "Moore", "given_name": "Gordon P.", "clpid": "Moore-G-P" }, { "family_name": "Scheller", "given_name": "Richard H.", "clpid": "Scheller-R-H" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The frequency of occurrence of particular repetitive sequence families has been estimated in the DNA of the three sea urchin species Strongylocentrotus purpuratus, Strongylocentrotus franciscanus and Lytechinus pictus using individual cloned S. purpuratus repetitive sequence elements. Cloned repetitive sequence elements as described by Scheller et al. (1977a) were prepared by reassociation of S. purpuratus DNA fragments to repetitive Cot, digestion with single-strand-specific nuclease S1 and ligation of synthetic restriction sites to their ends. The sequences were cloned by insertion at the Eco RI site of plasmid RSF2124, labeled, strand-separated and reassociated with 800\u2013900 nucleotide long unlabeled DNA. Both kinetic (genomic DNA excess) and saturation (cloned DNA excess) estimates of frequencies were made. For nine cloned fragments, the ratio of the repetition frequency in S. purpuratus DNA to that in S. franciscanus DNA ranges from about 20 to about 1. In the four cases examined, only a few copies were detected in the DNA of L. pictus. Estimates have also been made of frequency changes in many repetitive families by measuring the reassociation of labeled repetitive DNA fractions of each species with total DNA from other species. In each reciprocal comparison, the labeled repetitive sequences reassociate more slowly with DNA of other species than with DNA of the species from which they were prepared. Thus it appears that the dominant repetitive sequence families in the DNA of each species are present at lower frequencies in the DNA of closely related species. Measurements of thermal stability have been made of S. purpuratus cloned repetitive sequences reassociated with S. franciscanus DNA or S. purpuratus DNA. Most families have changed both in frequency and sequence, although some have changed little in sequence but show great changes in frequency.", "doi": "10.1016/0092-8674(78)90033-8", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1978-10", "series_number": "2", "volume": "15", "issue": "2", "pages": "649-660" }, { "id": "authors:bbnr2-4t104", "collection": "authors", "collection_id": "bbnr2-4t104", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-134909791", "type": "article", "title": "Specific representation of cloned repetitive DNA sequences in sea urchin RNAs", "author": [ { "family_name": "Scheller", "given_name": "Richard H.", "clpid": "Scheller-R-H" }, { "family_name": "Costantini", "given_name": "Franklin D.", "clpid": "Costantini-F-D" }, { "family_name": "Kozlowski", "given_name": "Michael R.", "clpid": "Kozlowski-M-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Nine cloned repetitive sequences were labeled, strand-separated and individually hybridized with RNA extracted from the nuclei of gastrula stage sea urchin embryos and of adult sea urchin intestine cells. The concentration of transcripts complementary to each cloned sequence was measured by RNA excess hybridization kinetics and by a DNA excess titration method. Transcripts of certain of the repeat families are present at over 100 times the concentration of transcripts of other families in each RNA. The set of repetitive sequence families highly represented in intestine nuclear RNA is different from that highly represented in gastrula nuclear RNA. Together with the results obtained with mature oocyte RNA and presented in the accompanying paper by Costantini et al. (1978), these findings show that quantitative patterns of repetitive sequence representation in RNA are specific to each cell type. Both strands of all of the nine cloned repeats are represented at some level in all the RNAs studied. Usually, though not always, the concentrations of transcripts complementary to the two strands of each repeat do not differ by more than a factor of two. The cloned tracers do not react with polysomal messenger RNA, and the nuclear RNA molecules with which they hybridize are many times larger than the repetitive sequences themselves.", "doi": "10.1016/0092-8674(78)90094-6", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1978-09", "series_number": "1", "volume": "15", "issue": "1", "pages": "189-203" }, { "id": "authors:yerzz-qrz77", "collection": "authors", "collection_id": "yerzz-qrz77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-135917880", "type": "article", "title": "Repetitive sequence transcripts in the mature sea urchin oocyte", "author": [ { "family_name": "Costantini", "given_name": "Franklin D.", "clpid": "Costantini-F-D" }, { "family_name": "Scheller", "given_name": "Richard H.", "clpid": "Scheller-R-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The expression of interspersed repetitive sequences in the RNA of mature sea urchin oocytes was investigated. ^3H-DNA tracers representing short interspersed repetitive sequences a few hundred nucleotides long, and long repetitive sequences approximately 2000 nucleotides long, were prepared from genomic DNA of the sea urchin, Strongylocentrotus purpuratus. These tracers were reacted with excess RNA from the mature oocyte. About 80% of the reactable short repeat tracer and 35% of the long repeat tracer hybridized. Thus most of the repetitive sequence families in the short repeat tracer are represented in oocyte RNA, and transcripts complementary to both strands of many repeat sequences are present. The kinetics of the reaction show that some transcripts are highly prevalent (>10^5 copies per oocyte), while others are rare (\u223c10^3 copies per oocyte). Nine cloned repetitive sequences were labeled, strand-separated and reacted with the oocyte RNA. Transcripts of both strands of all nine repeats were found in the RNA. The prevalence of transcripts of the cloned repeat families varied from \u223c3000 to 100,000 copies per oocyte. Studies with both cloned and genomic tracers show that transcript prevalence is independent of the genomic reiteration frequency of the transcribed repetitive sequences. Most of the families represented by prevalent transcripts have fewer than 200 copies per haploid genome. The RNA molecules with which the cloned repeats react are at least 1000\u20132000 nucleotides in length. Other experiments show that a majority of the members of repeat families represented by prevalent transcripts in the oocyte RNA are interspersed among single-copy sequence elements in the genome.", "doi": "10.1016/0092-8674(78)90093-4", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1978-09", "series_number": "1", "volume": "15", "issue": "1", "pages": "173-187" }, { "id": "authors:d7bap-py672", "collection": "authors", "collection_id": "d7bap-py672", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-141708874", "type": "article", "title": "Characteristics of individual repetitive sequence families in the sea urchin genome studied with cloned repeats", "author": [ { "family_name": "Klein", "given_name": "William H.", "clpid": "Klein-W-H" }, { "family_name": "Thomas", "given_name": "Terry L.", "clpid": "Thomas-T-L" }, { "family_name": "Lai", "given_name": "Cary", "clpid": "Lai-Cary" }, { "family_name": "Scheller", "given_name": "Richard H.", "clpid": "Scheller-R-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Cloned repetitive sequences from the S. purpuratus genome a few hundred to approximately 1000 nucleotides long were used to investigate the characteristics of individual repetitive sequence families. They were terminally labeled by the kinase procedure and reacted with sheared S. purpuratus DNA. Repetition frequencies were measured for 26 individual families and were found to vary from a few to several thousand copies per genome. Estimates of sequence divergence were made for 18 cloned repeat families by measuring thermal stability of the heteroduplexes formed between the genomic DNA and the cloned fragments, compared with that of the renatured cloned fragments. The difference was <4\u00b0C for three of the 18 families, and <10\u00b0C for 13 of the 18 families. These 13 repetitive sequence families lack any detectable highly divergent sequence relatives, and the results reported are shown not to change when the renaturation criterion is lowered below 55\u00b0C in 0.18 M Na^+. Five of the 18 cloned families displayed greater sequence divergence. The average sequence divergence of the total short repetitive sequence fraction of S. purpuratus DNA was found to match closely the average of the divergences of the cloned repeat sequences.", "doi": "10.1016/0092-8674(78)90344-6", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1978-08", "series_number": "4", "volume": "14", "issue": "4", "pages": "889-900" }, { "id": "authors:17ccj-kqt43", "collection": "authors", "collection_id": "17ccj-kqt43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-140621610", "type": "article", "title": "Sea urchin embryo mRNA sequences expressed in the nuclear RNA of adult tissues", "author": [ { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Klein", "given_name": "William H.", "clpid": "Klein-W-H" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The representation of message sequences in nuclear RNA was studied in sea urchin tissues which utilize these messages in their polysomes and in tissues which do not. A ^3H-labeled single-copy DNA tracer highly enriched for sequences complementary to blastula embryo mRNA was prepared. This tracer (mDNA) reacted to 78% with excess blastula mRNA, compared with 2.1% for the starting single-copy DNA. As expected from previous data, the mDNA reacted to only 12% with cytoplasmic RNA of adult intestine, since most embryo mRNA sequences are not detectable in this tissue. The mDNA reacted to the same extent, however, with nuclear RNA from either adult intestine, adult coelomocytes or gastrula embryos as with polysomal mRNA from blastula embryos. Thus virtually all of the blastula mRNA sequences are present in adult tissue nuclear RNAs, although most of these mRNA sequences are absent from cytoplasmic or polysomal RNA in the adult cells. The blastula mRNA sequences are present in heterogeneous nuclear RNAs at the same concentrations as are nuclear transcripts of most single-copy DNA sequences. Calculations based on the steady state concentration of structural gene transcripts in the embryo nuclei suggest that a majority of these molecules do not serve as message precursors.", "doi": "10.1016/0092-8674(78)90348-3", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1978-08", "series_number": "4", "volume": "14", "issue": "4", "pages": "941-950" }, { "id": "authors:7z33e-0dt49", "collection": "authors", "collection_id": "7z33e-0dt49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHAnar78", "type": "article", "title": "Studies on nucleic acid reassociation kinetics: V. Effects of disparity in tracer and driver fragment lengths", "author": [ { "family_name": "Chamberlin", "given_name": "Margaret E.", "clpid": "Chamberlin-M-E" }, { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Measurements are described of the kinetics of nucleic acid strand pair reassoci ation where the complementary strands are of different lengths and are present in different concentrations. Rate constants for the reaction of labelled fragments (\"tracer\") with excess complementary strands (\"driver\") were determined, both for driver fragment length greater than tracer fragment length and for the reverse case. Second order reactions and pseudo-first order reactions utilizing strand separated drivers and tracers were studied. The nucleic acids which served for this investigation were \u00d8X174 DNA and RNA, plasmid RSF2 124 DNA and E. coli DNA. Approximate empirical expressions relating driver and tracer fragment le\u00f1 the observed rate con stants were obtained for practical use. In long tracer-short driver reactions the ob served rate constant for the tracer reaction increases proportionately with tracer length. In long driver-short tracer reactions the rate of tracer reaction is retarded. The latter result is unexpected and appears to represent a departure from standard interpretations of the renaturation reaction.", "pmcid": "PMC342145", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "1978-06", "series_number": "6", "volume": "5", "issue": "6", "pages": "2073-2094" }, { "id": "authors:ygzd9-mfe70", "collection": "authors", "collection_id": "ygzd9-mfe70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151217-174102169", "type": "article", "title": "A large-scale laboratory maintenance system for gravid purple sea urchins (Strongylocentrotus purpuratus)", "author": [ { "family_name": "Leahy", "given_name": "Patrick S.", "clpid": "Leahy-P-S" }, { "family_name": "Tutschulte", "given_name": "Theodore C.", "clpid": "Tutschulte-T-C" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "A large-scale laboratory facility for the maintenance of several thousand gravid sea urchins (S. purpuratus) is described. Gametes of this species provide an important research resource for studies of animal development. Methods are described for culturing adult S. purpuratus for periods up to two years or more with almost no mortality after the first three to four weeks following collection. Adult females can be maintained in a fertile state in the culture system for four to six months. When spawned, gravid females living in the culture facility will routinely regenerate normal sized populations of fertile oocytes at 1 to 2-month intervals. Such females can be used repeatedly as a source of mature gametes for laboratory research. The reproductive performance of these females can be predicted approximately by the number of late vitellogenic oocytes present in their ovaries. After several months the pool of these oocytes is exhausted and no further mature oocytes can be found for a long period. We show, however, that such females are able to carry out a complete annual cycle of oogenesis if held for a long enough period of time in the culture system.", "doi": "10.1002/jez.1402040308", "issn": "0022-104X", "publisher": "Wiley-Liss Inc.", "publication": "Journal of Experimental Zoology", "publication_date": "1978-06", "series_number": "3", "volume": "204", "issue": "3", "pages": "369-380" }, { "id": "authors:vmt5v-kf768", "collection": "authors", "collection_id": "vmt5v-kf768", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-121017620", "type": "article", "title": "Primate Evolution: Molecular Anthropology. Genes and Proteins in the Evolutionary Ascent of the Primates. Papers from a symposium, Burg Wartenstein, Austria, July 1975. Morris Goodman, Richard E. Tashian, and Jeanne H. Tashian, Eds. Plenum, New York, 1976. [Book Review]", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "[No Abstract]", "doi": "10.1126/science.198.4314.286.b", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1977-10-21", "series_number": "4314", "volume": "198", "issue": "4314", "pages": "286-287" }, { "id": "authors:y0qac-w6m14", "collection": "authors", "collection_id": "y0qac-w6m14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-143901784", "type": "article", "title": "Appearance and persistence of maternal RNA sequences in sea urchin development", "author": [ { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Ernst", "given_name": "Susan G.", "clpid": "Ernst-S-G" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "This paper deals with the relationship between the single copy transcripts represented in mature oocytes of the sea urchin and the RNA sequences present in immature oocytes and embryos. We term the oocyte transcripts from single copy DNA the maternal single copy sequence set. A single copy [^3H]DNA fraction ([^3H]oDNA) enriched for sequences complementary to the maternal single copy sequence set was prepared and reacted with the different RNA preparations. The complexity of the mature oocyte RNA is estimated to be 37 \u00d7 10^6 nucleotides. At kinetic termination, [3H]oDNA reacted with the polysomal mRNA of 16-cell embryos to 73% of the reaction with mature oocyte RNA, indicating that 27 \u00d7 10^6 nucleotides of the maternal sequence set are present. With blastula mRNA the reaction equals about 56%, a complexity of 21 \u00d7 10^6 nucleotides; with gastrula mRNA, 53%, a complexity of 19 \u00d7 10^6 nucleotides. The relative amount of hybridization of [^3H]oDNA was 100% with cytoplasmic RNA of the 16-cell stage and became progressively less with the cytoplasmic RNAs of later stages. The total RNA of immature oocytes was found to include about 26 \u00d7 10^6 nucleotides of the maternal sequence set. Results of these experiments are discussed, and an interpretation of the pattern of utilization of structural genes during oocyte and embryo development is suggested.", "doi": "10.1016/0012-1606(77)90123-3", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1977-10", "series_number": "1", "volume": "60", "issue": "1", "pages": "258-277" }, { "id": "authors:kb2k9-p7b82", "collection": "authors", "collection_id": "kb2k9-p7b82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:PEAnar77", "type": "article", "title": "A program for least squares analysis of reassociation and hybridization data", "author": [ { "family_name": "Pearson", "given_name": "W. R.", "clpid": "Pearson-W-R" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" } ], "abstract": "A computer program is described for the rapid calculation of least squares solutions for data fitted to different functions normally used in reassociation and hybridization kinetic measurements. The equations for the fraction not reacted as a function of Cot follow: First order, exp(\u2013kCot); second order, (1+kCot)\u20131 ; variable order, (1+kCot)\u2013n; approximate fraction of DNA sequence remaining single stranded, (1+kCot)\u201344; and a function describing the pairing of tracer when the rate constant for the tracer (k) is distinct from the driver rate constant kd): exp{kL1-(1+kdCot)1\u2013nJ/Lkd(1-n)J}. Several components may be used for most of these functional forms. The standard deviations of the individual parameters at the solutions are calculated.", "doi": "10.1093/nar/4.6.1727", "pmcid": "PMC342517", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "1977-06", "series_number": "6", "volume": "4", "issue": "6", "pages": "1727-1737" }, { "id": "authors:ny412-x5323", "collection": "authors", "collection_id": "ny412-x5323", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:EDEnar77", "type": "article", "title": "Exploration of long and short repetitive sequence relationships in the sea urchin genome", "author": [ { "family_name": "Eden", "given_name": "Francine C.", "clpid": "Eden-F-C" }, { "family_name": "Graham", "given_name": "Dale E.", "clpid": "Graham-D-E" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Long and short repetitive sequences of sea urchin DNA were prepared by reassoci-ation of 2000 nucleotide long fragments to Cot 4 and digestion with the single strand specific nuclease S1. The S1 resistant duplexes were separated into long repetitive and short repetitive fractions on Agarose A50. The extent of shared sequences was studied by reassociating a labeled preparation of short repetitive DNA with an excess of unlabeled long repetitive DNA. Less than 10% of the long repetitive DNA preparation was able to reassociate with the short repetitive DNA. Thus the long and short repetitive elements appear to be principally independent sequence classes in sea urchin DNA. \n\nPrecisely reassociating repetitive DNA was prepared by four successive steps of reassociation and thermal chromatography on hydroxyapatite. This fraction (3% of the genome) was reassociated by itself or with a great excess of total sea urchin DNA. The thermal stability of the products was identical in both cases (Tm=81\u00b0C), indicating that precisely repeated sequences do not have many imprecise copies in sea urchin DNA.", "doi": "10.1093/nar/4.5.1553", "pmcid": "PMC343773", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "1977-06", "series_number": "5", "volume": "4", "issue": "5", "pages": "1553-1567" }, { "id": "authors:q79rs-trb19", "collection": "authors", "collection_id": "q79rs-trb19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GALpnas77b", "type": "article", "title": "Studies on Nucleic Acid Reassociation Kinetics: Retarded Rate of Hybridization of RNA with Excess DNA", "author": [ { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Smith", "given_name": "Michael J.", "clpid": "Smith-M-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The rate of reaction of excess double-stranded bacteriophage phi X174 and plasmid RSF2124 DNA drivers with enzymatically synthesized asymmetric RNA tracers was measured. Other reactions were carried out with excess Escherichia coli DNA and E. coli RNA labeled in vivo. RNA and DNA fragment lengths were held approximately equal. For each case it was shown that in DNA excess the rate constant for RNA\u00b7 DNA hybridization is 3- to 4.5-fold lower than that of the renaturation rate constant for the driver DNA. This retardation was also observed in pseudo-first-order hybridization reactions driven by excess strand-separated RSF2124 DNA. It was concluded that the rate constant for RNA\u00b7 DNA hybridization depends partially on which species is in excess.", "pmcid": "PMC432159", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1977-06", "series_number": "6", "volume": "74", "issue": "6", "pages": "2306-2310" }, { "id": "authors:pc2dy-bdp72", "collection": "authors", "collection_id": "pc2dy-bdp72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151116-151633381", "type": "article", "title": "Interspersion of short repetitive sequences studied in cloned sea urchin DNA fragments", "author": [ { "family_name": "Lee", "given_name": "Amy S.", "clpid": "Lee-A-S" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The length and spacing of repetitive sequence elements were studied in several cloned sea urchin DNA fragments. Sequence organization in these fragments was found to be of the short interspersed form expected for sea urchin DNA, and for one clone the evidence shows that nearby repeats do not belong to the same repetitive sequence family.", "doi": "10.1126/science.847465", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1977-04-08", "series_number": "4286", "volume": "196", "issue": "4286", "pages": "189-192" }, { "id": "authors:32m1q-05b54", "collection": "authors", "collection_id": "32m1q-05b54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150630-123440728", "type": "article", "title": "Clones of individual repetitive sequences from sea urchin DNA constructed with synthetic Eco RI sites", "author": [ { "family_name": "Scheller", "given_name": "Richard H.", "clpid": "Scheller-R-H" }, { "family_name": "Thomas", "given_name": "Terry L.", "clpid": "Thomas-T-L" }, { "family_name": "Lee", "given_name": "Amy S.", "clpid": "Lee-A-S" }, { "family_name": "Klein", "given_name": "William H.", "clpid": "Klein-W-H" }, { "family_name": "Niles", "given_name": "Walter D.", "clpid": "Niles-W-D" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Interspersed repetitive sequences were isolated from sea urchin DNA by renaturing to low C_0t followed by treatment with nuclease SI. Synthetic Eco RI sites were ligated onto the repetitive sequence elements, which were then inserted at the Eco RI site of plasmid RSF2124 and cloned. The repetitive sequences can be excised from the plasmid with Eco RI for further study.", "doi": "10.1126/science.847467", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1977-04-08", "series_number": "4286", "volume": "196", "issue": "4286", "pages": "197-200" }, { "id": "authors:2geyy-rwp86", "collection": "authors", "collection_id": "2geyy-rwp86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GALpnas77a", "type": "article", "title": "Studies on Nucleic Acid Reassociation Kinetics: Rate of Hybridization of Excess RNA with DNA, Compared to the Rate of DNA Renaturation", "author": [ { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The rate of reaction of double-stranded replicative form (RF)[3H]DNA of bacteriophage phi X174 with excess (+)strand DNA and (+)strand RNA was measured by standard methods of hydroxyapatite chromatography. The reactions follow pseudo-first-order kinetics and the observed rate constant for the RNA\u00b7 DNA reaction differs less than 25% from that of the DNA\u00b7 DNA reaction. The pseudo-first-order rate constants are close to the value predicted on the basis of the second-order rate constant measured in the renaturation of the double-stranded phi X RF [3H]DNA.", "pmcid": "PMC430570", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1977-03", "series_number": "3", "volume": "74", "issue": "3", "pages": "1020-1023" }, { "id": "authors:n2fsq-5a093", "collection": "authors", "collection_id": "n2fsq-5a093", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160812-124415301", "type": "article", "title": "Synthesis and turnover of polysomal mRNAs in sea urchin embryos", "author": [ { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Lipson", "given_name": "Edward D.", "clpid": "Lipson-E-D" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The synthesis and turnover kinetics of polysomal mRNA have been measured in sea urchin embryos. Polysomes were isolated from stages ranging between mesenchyme blastula and late gastrula Strongylocentrotus purpuratus embryos which had been exposed to exogenous ^3H-guanosine. The amount of radioactivity incorporated into messenger and ribosomal RNAs was determined separately as a function of time, and the precursor pool specific activity was measured in the same embryos. Synthesis and decay rate constants were extracted from the data by a leastsquares procedure. Per embryo, the rate of mRNA synthesis was calculated to be about 0.13 pg min_(\u22121), while the rate of rRNA synthesis is about 0.022 pg min^(\u22121). The newly synthesized mRNA turns over with a half-time of 5.7 hr. The data support only a single decay rate for the mRNA, but small fractions of mRNA decaying at different rates cannot be excluded. Previous studies have shown that a minor fraction of the mRNA includes the least abundant, most highly diverse set of messages (\"complex class\" mRNAs). To determine whether mRNAs of the complex class are synthesized and degraded at similar rates, labeled mRNA was measured in hybrids formed in mRNA excess reactions with single copy DNA. These experiments showed that complex class mRNAs represent an approximately proportional amount of the new mRNA synthesis, and turn over at the same average rate as does the bulk of the mRNA. Most of the mRNAs in the embryo polysomes are newly synthesized, rather than maternal. This statement refers both to complex class mRNAs and to prevalent mRNAs. Considering the sequence homology between embryo and oocyte mRNAs shown earlier, these results indicate that many of the same structural genes active during oogenesis are being transcribed in embryos at these stages.", "doi": "10.1016/0092-8674(77)90029-0", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1977-03", "series_number": "3", "volume": "10", "issue": "3", "pages": "415-432" }, { "id": "authors:vet4b-qqz74", "collection": "authors", "collection_id": "vet4b-qqz74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160418-085641040", "type": "article", "title": "Significance of rare mRNA sequences in liver", "author": [ { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Klein", "given_name": "William H.", "clpid": "Klein-W-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "From mRNA-DNA hybridization studies it is known that eukaryotic mRNAs occur in several abundance classes. One such study with mammalian liver mRNA indicates that in this tissue the most complex abundance class consists of messenger RNAs present in 5\u201340 copies per cell. The other abundance classes are less complex and consist of mRNA sequences present an average of 250 and 7200 times per cell. In this paper we summarize approximate calculations of the number of mRNA molecules needed to sustain the steady-state quantities of 40 rodent liver proteins. Data were obtained from the literature regarding subunit molecular weights, degradation rate constants, and the concentration of each of these proteins in liver. The sample of proteins was chosen simply on the basis of the availability of the relevant data in the literature. For 13 of these proteins more direct estimates of mRNA frequency per cell could also be derived from measurements of the fraction of total protein synthesis accounted for by the protein in question. In all cases these estimates agreed within a factor of 2 to 3 with the values calculated from protein concentration and turnover rates. Several proteins known to be expressed in a histospecific way in liver were found to require steady-state mRNA concentrations in the range of only 1\u201330 copies per cell. This suggests that at least some of the mRNAs in the lowest abundance class are present as the result of the specific regulation of structural gene transcription.", "doi": "10.1016/0003-9861(77)90147-3", "issn": "0003-9861", "publisher": "Academic Press", "publication": "Archives of Biochemistry and Biophysics", "publication_date": "1977-03", "series_number": "2", "volume": "179", "issue": "2", "pages": "584-599" }, { "id": "authors:s55k2-pbf21", "collection": "authors", "collection_id": "s55k2-pbf21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160802-115919217", "type": "article", "title": "Sequence organization in animal DNA and a speculation on hnRNA as a coordinate regulatory transcript", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Klein", "given_name": "William H.", "clpid": "Klein-W-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The proposal is made that hnRNA is a coordinate regulatory transcript consisting principally of repetitive regulatory sequences and single-copy spacer sequences. The large transcription units characteristic of animal cells are interpreted as mechanisms for ensuring transcription of multiple regulatory signals under the control of single initiation sites. This organization of transcription is conceived to be a part of the system which integrates the control of gene expression. Animal DNA sequence organization is considered in this light and various consequences of these ideas are explored. Some testable predictions are developed for two cases: (a) that the regulatory signals are diffusible RNA activators originating from the short repetitive sequences interspersed in hnRNA and (b) that the regulatory signals are protein activators coded by message sequences embedded in the hnRNA transcript.", "doi": "10.1016/0012-1606(77)90320-7", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1977-01", "series_number": "1", "volume": "55", "issue": "1", "pages": "69-84" }, { "id": "authors:ws2jz-4c243", "collection": "authors", "collection_id": "ws2jz-4c243", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151216-172238139", "type": "article", "title": "Absence of short period interspersion of repetitive and non-repetitive sequences in the DNA of Drosophila melanogaster", "author": [ { "family_name": "Crain", "given_name": "William R.", "clpid": "Crain-W-R-Jr" }, { "family_name": "Eden", "given_name": "Francine C.", "clpid": "Eden-F-C" }, { "family_name": "Pearson", "given_name": "William R.", "clpid": "Pearson-W-R" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "A sensitive search has been made in Drosophila melanogaster DNA for short repetitive sequences interspersed with single copy sequences. Five kinds of measurements all yield the conclusion that there are few short repetitive sequences in this genome: 1) Comparison of the kinetics of reassociation of short (360 nucleotide) and long (1,830 nucleotide) fragments of DNA; 2) reassociation kinetics of long fragments (2,200 nucleotide) with an excess of short (390 short nucleotide) fragments; 3) measurement of the size of S1 nuclease resistant reassociated repeated sequences; 4) measurement of the hyperchromicity of reassociated repetitive fragments as a function of length; 5) direct assay by kinetics of reassociation of the amount of single copy sequence present on 1,200 nucleotide long fragments which also contain repetitive sequences.", "doi": "10.1007/BF00292953", "issn": "0009-5915", "publisher": "Springer", "publication": "Chromosoma", "publication_date": "1976-12", "series_number": "4", "volume": "56", "issue": "4", "pages": "309-326" }, { "id": "authors:4xehq-zwr06", "collection": "authors", "collection_id": "4xehq-zwr06", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151216-172028874", "type": "article", "title": "Single copy DNA and structural gene sequence relationships among four sea urchin species", "author": [ { "family_name": "Angerer", "given_name": "Robert C.", "clpid": "Angerer-R-C" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Measurements of the divergence of single copy DNA sequences among four sea urchin species are presented. At a standard criterion for reassociation (0.12 M phosphate buffer, 60\u00b0 C, hydroxyapatite binding) we observe the following extents of reaction and reductions in thermal stability for single copy DNA reassociation between Strongylocentrotus purpuratus tracer and heterologous driver DNA: S. dr\u00f6bachiensis 68% and 2.5\u00b0C; S. franciscanus 51% and 3.5\u00b0 C; Lytechinus pictus 12% and 7.5\u00b0 C. The implied extents of sequence relatedness are consistent with the phylogenetic relationships of these species. The rate of single copy sequence divergence in the evolutionary lines leading to the Strongylocentrotus species is estimated to be 0.06\u20130.35% per million years. The rate of divergence of total single copy sequence has been compared to that of structural gene sequences represented in S. purpuratus gastrula polysomal messenger RNA. When closely related species, S. purpuratus and S. franciscanus, are compared, these polysomal sequences are found to diverge at a lower rate than does the total single copy sequence. For two very distantly related species, S. purpuratus and L. pictus, a small fraction of the single copy DNA sequence is probably conserved. These conserved sequences are not enriched in their content of structural gene sequences.", "doi": "10.1007/BF00293186", "issn": "0009-5915", "publisher": "Springer", "publication": "Chromosoma", "publication_date": "1976-09", "series_number": "3", "volume": "56", "issue": "3", "pages": "213-226" }, { "id": "authors:avv2x-wd259", "collection": "authors", "collection_id": "avv2x-wd259", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160802-140947033", "type": "article", "title": "Sequence complexity of the RNA accumulated in Oocytes of Arbacia punctulata", "author": [ { "family_name": "Anderson", "given_name": "David M.", "clpid": "Anderson-D-M" }, { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The sequence complexity of the RNA present in mature oocytes of the sea urchin Arbacia punctulata was measured by DNA-RNA hybridization. Small quantities of single copy [^3H]DNA were hybridized with large excesses of RNA and the amount of [^3H]DNA-RNA hybrids formed was assayed by hydroxyapatite. At termination of the reaction, which follows pseudo-first-order kinetics, 2.6% of the reactable single copy [^3H]DNA mass is present in RNA-DNA hybrids. This DNA was isolated, shown to be rehybridizable to RNA and, within the range of detectability, to consist solely of nonrepetitive sequences. Assuming asymmetric transcription, 5.2% of the genomic single copy sequence, or 3.0 \u00d7 10^7 nucleotides, is represented in oocyte RNA. The kinetics of hybridization indicate that these sequences are included in approximately 1\u20132% of the oocyte RNA.", "doi": "10.1016/0012-1606(76)90128-7", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1976-07-01", "series_number": "1", "volume": "51", "issue": "1", "pages": "138-145" }, { "id": "authors:c348x-xhg18", "collection": "authors", "collection_id": "c348x-xhg18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:EFSpnas76", "type": "article", "title": "DNA Sequence Organization in the Lepidopteran Antheraea pernyi", "author": [ { "family_name": "Efstratiadis", "given_name": "A.", "clpid": "Efstratiadis-A" }, { "family_name": "Crain", "given_name": "W. R.", "clpid": "Crain-W-R-Jr" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" }, { "family_name": "Kafatos", "given_name": "F. C.", "clpid": "Kafatos-F-C" } ], "abstract": "A large fraction of the genome of the lepidopteran Antheraea pernyi consists of interspersed single-copy sequences and repetitive DNA sequences of 300 nucleotide average length. Most of the single-copy sequences are about 800 nucleotides long and a minority are considerably longer. Thus, the organization of the DNA sequences of this insect is similar to that of most higher organisms and different from that of Drosophila.", "pmcid": "PMC430533", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1976-07", "series_number": "7", "volume": "73", "issue": "7", "pages": "2289-2293" }, { "id": "authors:fc9hb-z0254", "collection": "authors", "collection_id": "fc9hb-z0254", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160812-134923037", "type": "article", "title": "Structural Gene Sets Active in Embryos and Adult Tissues of the Sea Urchin", "author": [ { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Klein", "given_name": "William H.", "clpid": "Klein-W-H" }, { "family_name": "Davis", "given_name": "Mark M.", "clpid": "Davis-M-M" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Structural gene sequences active in a variety of sea urchin adult and embryo tissues are compared. A single-copy ^3H-DNA fraction, termed mDNA, was isolated, which contains sequences complementary to the messenger RNA present on gastrula stage polysomes. Gastrula message sequences are 50 fold concentrated in the mDNA compared to total single-copy DNA. mDNA reactions were carried out with excess mRNA from blastula, pluteus, exogastrula, adult ovary, tubefoot, intestine, and coelomocytes, and with excess total mature oocyte RNA. A single-copy ^3H-DNA fraction totally devoid of gastrula message sequences, termed null mDNA, was also reacted with these RNAs. Large differences in the extent of both mDNA and null mDNA reaction with the various RNAs were observed, indicating that in each state of differention a distinct set of structural genes is active, generally characterized by several thousand specific sequences. The complexity of gastrula mRNA was shown in previous work to be about 17 \u00d7 10^6 nucleotides. In units of 10^6 nucleotides, the complexities of the RNA sequence reacting with mDNA and with null mDNA in each tissue are, respectively, as follows: intestine mRNA; 2.1 and 3.7; coelomocyte mRNA: 3.5 and \u22641.4; tubefoot mRNA: 2.7 and \u22640.4; ovary mRNA: 13 and 6.7; oocyte total RNA: 17 and 20; blastula mRNA: 12 and 15; pluteus mRNA: 14 and \u22640.6; exogastrula mRNA: 14 and \u22640.6. The total complexity of each mRNA population is the sum of these values, as verified for several cases by reactions with total single-copy DNA. A relatively small set of mRNAs, the complexity of which is about 2.1 \u00d7 10^6 nucleotides, appears to be shared by several of the tissues studied.", "doi": "10.1016/0092-8674(76)90200-2", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1976-04", "series_number": "4", "volume": "7", "issue": "4", "pages": "487-505" }, { "id": "authors:h3kr7-rkf97", "collection": "authors", "collection_id": "h3kr7-rkf97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151216-172536463", "type": "article", "title": "Contrasting patterns of DNA sequence arrangement in Apis mellifera (Honeybee) and Musca domestica (housefly)", "author": [ { "family_name": "Crain", "given_name": "William R.", "clpid": "Crain-W-R-Jr" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "We have examined the organization of the repeated and single copy DNA sequences in the genomes of two insects, the honeybee (Apis mellifera) and the housefly (Musca domestica). Analysis of the reassociation kinetics of honeybee DNA fragments 330 and 2,200 nucleotides long shows that approximately 90% of both size fragments is composed entirely of non-repeated sequences. Thus honeybee DNA contains few or no repeated sequences interspersed with nonrepeated sequences at a distance of less than a few thousand nucleotides. On the other hand, the reassociation kinetics of housefly DNA fragments 250 and 2,000 nucleotides long indicates that less than 15% of the longer fragments are composed entirely of single copy sequences. A large fraction of the housefly DNA therefore contains repeated sequences spaced less than a few thousand nucleotides apart. Reassociated repetitive DNA from the housefly was treated with S1 nuclease and sized on agarose A-50. The S1 resistant sequences have a bimodal distribution of lengths. Thirty-three percent is greater than 1,500 nucleotide pairs, and 67% has an average size about 300 nucleotide pairs. The genome of the housefly appears to have at least 70% of its DNA arranged as short repeats interspersed with single copy sequences in a pattern qualitatively similar to that of most eukaryotic genomes.", "doi": "10.1007/BF00327705", "issn": "0009-5915", "publisher": "Springer", "publication": "Chromosoma", "publication_date": "1976-03", "series_number": "1", "volume": "59", "issue": "1", "pages": "1-12" }, { "id": "authors:3yc9d-9q963", "collection": "authors", "collection_id": "3yc9d-9q963", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151216-172822557", "type": "article", "title": "Evolutionary divergence and length of repetitive sequences in sea urchin DNA", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Graham", "given_name": "Dale E.", "clpid": "Graham-D-E" }, { "family_name": "Eden", "given_name": "Francine C.", "clpid": "Eden-F-C" }, { "family_name": "Painchaud", "given_name": "Denise M.", "clpid": "Painchaud-D-M" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The organization of repetitive and single copy DNA sequences in sea urchin DNA has been examined with the single strand specific nuclease Sl fromAspergillus. Conditions and levels of enzyme were established so that single strand DNA was effectively digested while reassociated divergent repetitive duplexes remained enzyme resistant. About 25% of sea urchin DNA reassociates with repetitive kinetics to form Sl resistant duplexes of two distinct size classes derived from long and short repetitive sequences in the sea urchin genome. Fragments 2,000 nucleotides long were reassociated to Cot 20 and subjected to controlled digestion with Sl nuclease. About half of the resistant duplexes (13% of the DNA) are short, with a mode size of about 300 nucleotide pairs. This class exhibits significant sequence divergence, and principally consists of repetitive sequences which were interspersed with single copy sequences. About one-third of the long duplexes (4% of the DNA) are reduced in size after extensive Sl nuclease digestion to about 300 nucleotide pairs. About two-thirds of the long resistant duplexes (8% of the DNA) remains long after extensive SI nuclease digestion. These long reassociated duplexes are precisely base paired. The short duplexes are imprecisely paired with a melting temperature about 9\u00b0C below that of precisely paired duplexes of the same length. The relationship between length of repetitive duplex and precision of repetition is confirmed by an independent method and has been observed in the DNA of a number of species over a wide phylogenetic area.", "doi": "10.1007/BF01796119", "issn": "0022-2844", "publisher": "Springer Verlag", "publication": "Journal of Molecular Evolution", "publication_date": "1976-03", "series_number": "1", "volume": "9", "issue": "1", "pages": "1-23" }, { "id": "authors:vxz2p-8n412", "collection": "authors", "collection_id": "vxz2p-8n412", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas76", "type": "article", "title": "Studies on nucleic acid reassociation kinetics: empirical equations describing DNA reassociation", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The rate of appearance of duplex DNA renaturation, measured with single strand specific nuclease, deviates significantly from a second order reaction. Measurements reported in paper I of this series indicate an inhibition in the rate of reassociation of single strand tails on partially reassociated molecules by a factor of at least two. Equations are derived that describe the observed form of reassociation kinetics as measured with hydroxyapatite and with single strand specific nuclease. The free parameter that describes the extent of inhibition of nucleation with single strand tails in these equations has been evaluated by least squares methods and agrees with the experimentally measured value.", "pmcid": "PMC335919", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1976-02", "series_number": "2", "volume": "73", "issue": "2", "pages": "415-419" }, { "id": "authors:00r14-nb444", "collection": "authors", "collection_id": "00r14-nb444", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SMIpnas75", "type": "article", "title": "Studies on nucleic acid reassociation kinetics: Reactivity of single-stranded tails in DNA-DNA renaturation", "author": [ { "family_name": "Smith", "given_name": "Michael J.", "clpid": "Smith-M-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The reassociation kinetics of Escherichia coli DNA were measured by S1 nuclease resistance and hydroxyapatite binding. While the reaction assayed by hydroxyapatite displays second order kinetics, the S1 nuclease measurements follow a non-second order form, as previously reported by Morrow (Ph.D. Dissertation, Stanford University, 1974). Much of the reaction measured with S1 nuclease occurs between single stranded regions of fragments already bearing duplex structures from previous collisions, and between such regions and totally free single strands. Experimental determinations indicate that the nucleation rate of single stranded regions on fragments also containing duplexes is inhibited by an average factor of 2 to 4.", "pmcid": "PMC388820", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1975-12", "series_number": "12", "volume": "72", "issue": "12", "pages": "4805-4809" }, { "id": "authors:w17v9-5fr98", "collection": "authors", "collection_id": "w17v9-5fr98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151216-171159084", "type": "article", "title": "Comparative aspects of DNA organization in metazoa", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Angerer", "given_name": "Robert C.", "clpid": "Angerer-R-C" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Data on sequence organization in metazoa are reviewed and tabulated. It is shown that the features of sequence organization previously observed in Xenopus DNA are extremely widespread. At least 70% of DNA fragments 2,000\u20133,000 nucleotides long contain both single copy and repetitive sequence in all the organisms examined except Drosophila.", "doi": "10.1007/BF00284818", "issn": "0009-5915", "publisher": "Springer", "publication": "Chromosoma", "publication_date": "1975-09", "series_number": "3", "volume": "51", "issue": "3", "pages": "253-259" }, { "id": "authors:7dkfp-4kr52", "collection": "authors", "collection_id": "7dkfp-4kr52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160811-071702871", "type": "article", "title": "DNA Sequence Organization in the Mollusc Aplysia Californica", "author": [ { "family_name": "Angerer", "given_name": "Robert C.", "clpid": "Angerer-R-C" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The sequence organization of the DNA of the mollusc Aplysia californica has been examined by a combination of techniques. Close-spaced interspersion of repetitive and single copy sequences occurs throughout the majority of the genome. Detailed examination of the DNA of this protostome reveals great similarities to the pattern observed in the two deuterostome organisms previously examined in detail in this laboratory, Xenopus laevis and Strongylocentrotus purpuratus. Labeled and unlabeled Aplysia DNA were prepared from developing embryos and sheared to a fragment length of 400 nucleotides. The kinetics of reassociation were studied by means of hydroxyapatite chromatography, single-strand-specific S1 nuclease, and optical methods of assay. Aplysia DNA of this fragment length contains at least five resolvable kinetic fractions. One classification of these fractions, listed with their reassociation rate constants (I M\u22121 sec\u22121) is: single copy (0.00057), slow (0.047), fast (2.58), very fast (4000), and foldback (> 105).\nSequence arrangement was deduced from: the kinetics of reassociation of DNA fragments of length 400 or 2000 nucleotides; the hyperchromicity of reassociated fragments containing duplex regions; the size of duplex regions resistant to S1 nuclease; and the reassociation of labeled fragments of various lengths with short driver fragments.\nMore than 80% of the single copy DNA sequences are interspersed with repetitive sequences. The maximum spacing of the repeats is about 2000 nucleotides, and the average less than 1000. The very fast fraction does not show interspersion with single copy sequences or with other kinetic fractions. The foldback fraction sequences are fairly widely interspersed. The slow fraction sequences are interspersed with the fast fraction, and possibly also with the single copy DNA. The fast fraction is the dominant interspersed repetitive fraction. Its sequences are adjacent to the great majority of the single copy sequences and have an average length of about 300 nucleotides.", "doi": "10.1016/0092-8674(75)90070-7", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1975-09", "series_number": "1", "volume": "6", "issue": "1", "pages": "29-40" }, { "id": "authors:z55yn-45704", "collection": "authors", "collection_id": "z55yn-45704", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151216-170610841", "type": "article", "title": "DNA sequence organization in the genomes of five marine invertebrates", "author": [ { "family_name": "Goldberg", "given_name": "Robert B.", "clpid": "Goldberg-R-B" }, { "family_name": "Crain", "given_name": "William R.", "clpid": "Crain-W-R-Jr" }, { "family_name": "Ruderman", "given_name": "Joan V.", "clpid": "Ruderman-J-V" }, { "family_name": "Moore", "given_name": "Gordon P.", "clpid": "Moore-G-P" }, { "family_name": "Barnett", "given_name": "Thomas R.", "clpid": "Barnett-T-R" }, { "family_name": "Higgins", "given_name": "Ratchford C.", "clpid": "Higgins-R-C" }, { "family_name": "Gelfand", "given_name": "Robert A.", "clpid": "Gelfand-R-A" }, { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The arrangement of repetitive and non-repetitive sequence was studied in the genomic DNA of the oyster (Crassostrea virginica), the surf clam (Spisula solidissima), the horseshoe crab (Limulus polyphemus), a nemertean worm (Cerebratulus lacteus) and a jellyfish (Aurelia aurita). Except for the jellyfish these animals belong to the protostomial branch of animal evolution, for which little information regarding DNA sequence organization has previously been available. The reassociation kinetics of short (250\u2013300 nucleotide) and long (2,000\u20133,000 nucleotide) DNA fragments was studied by the hydroxyapatite method. It was shown that in each case a major fraction of the DNA consists of single copy sequences less than about 3,000 nucleotides in length, interspersed with short repetitive sequences. The lengths of the repetitive sequences were estimated by optical hyperchromicity and S1 nuclease measurements made on renaturation products. All the genomes studied include a prominent fraction of interspersed repetitive sequences about 300 nucleotides in length, as well as longer repetitive sequence regions.", "doi": "10.1007/BF00284817", "issn": "0009-5915", "publisher": "Springer", "publication": "Chromosoma", "publication_date": "1975-09", "series_number": "3", "volume": "51", "issue": "3", "pages": "225-251" }, { "id": "authors:a7tr7-fbx47", "collection": "authors", "collection_id": "a7tr7-fbx47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160805-112703291", "type": "article", "title": "Sequence Organization in Xenopus DNA Studied by the Electron Microscope", "author": [ { "family_name": "Chamberlin", "given_name": "Margaret E.", "clpid": "Chamberlin-M-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Xenopus laevis DNA was extracted from red blood cells and sheared to a mean length of 2780 nucleotides. The DNA was stripped of foldback-containing fragments and incubated to C_0t 10 (mol \u00b7 s \u00b7 l^(\u22121)), allowing most repetitive sequences to form duplex structures. Duplex-containing fragments were eluted from an hydroxylapatite column and visualized for electron microscopy by spreading from 57% formamide according to the modified Kleinschmidt technique of Davis et al. (1971). The mean length of the fragments observed was 2445 nucleotides. A total of 1700 DNA strands were photographed and studied. Less than 5% of the total strand length was in uninterpretable structures. Every molecule falling within the confines of the plates was included in the sample. Over 50% of the total strand length in the sample was found in structures bearing at least one interspersed repetitive sequence duplex terminated by four single-strand regions. The fraction of DNA present in duplex regions was almost exactly that predicted if the duplex regions represent all the interspersed middle repetitive sequence in the Xenopus genome. Direct measurement of visualized duplexes shows that the mean length of interspersed repetitive sequence elements in this genome is 345 nucleotides. Duplex length was shown to be independent of the length of the strands bearing the duplexes. These observations provide direct confirmation of the length of approximately 300 nucleotides indicated for interspersed repetitive sequences by earlier physical-chemical studies 011 Xenopus DNA. In strands carrying two duplexes terminated by single-strand regions the interduplex, or single-copy sequence element length could be measured. Sequence interspersion curves generated from these data are roughly consistent with those derived earlier from measurements of hydroxylapatite binding as a function of fragment length.", "doi": "10.1016/0022-2836(75)90351-4", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1975-08-05", "series_number": "2", "volume": "96", "issue": "2", "pages": "317-333" }, { "id": "authors:t8wq9-t9d42", "collection": "authors", "collection_id": "t8wq9-t9d42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160801-114124466", "type": "article", "title": "Sequence complexity of heterogeneous nuclear RNA in sea urchin embryos", "author": [ { "family_name": "Hough", "given_name": "Barbara R.", "clpid": "Hough-B-R" }, { "family_name": "Smith", "given_name": "Michael J.", "clpid": "Smith-M-J" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The sequence complexity of heterogeneous nuclear RNA in sea urchin gastrulas was measured by RNA-driven hybridization reactions with nonrepetitive sea urchin DNA. 28.5% of the sequence complexity of the genome is represented in the nuclear RNA. This amounts to 1.74 \u00d7 10^8 nucleotides of diverse sequence, more than 10 times the nucleotide complexity of the polysomal messenger RNA extracted from sea urchin embryos at the same stage. The complex set of nuclear RNA sequences driving this hybridization reaction was shown to be the same as the rapidly labeled hnRNA, using pulse-labeled nuclear RNA as driver.", "doi": "10.1016/0092-8674(75)90104-X", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1975-07", "series_number": "3", "volume": "5", "issue": "3", "pages": "291-299" }, { "id": "authors:nt8mm-e6118", "collection": "authors", "collection_id": "nt8mm-e6118", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160810-150351368", "type": "article", "title": "Structural genes adjacent to interspersed repetitive DNA sequences", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Klein", "given_name": "William H.", "clpid": "Klein-W-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The observation that repetitive and single copy sequences are interspersed in animal DNAs has suggested that repetitive sequences are adjacent to single copy structural gene sequences. To test this concept, single copy DNA sequences contiguous to interspersed repetitive sequences were prepared from sea urchin DNA by hydroxyapatite fractionation (repeat-contiguous DNA fraction). These single copy sequences included about one third of the total nonrepetitive sequence in the genome as determined by the amounts recovered during the hydroxyapatite fractionation and by reassociation kinetics. 3H-labeled mRNA from sea urchin gastrula was prepared by puromycin release from polysomes and used in DNA-driven hybridization reactions. The kinetics of mRNA hybridization reactions with excess whole DNA were carefully measured, and the rate of hybridization was found to be 3\u20135 times slower than the corresponding single copy DNA driver reassociation rate. The mRNA hybridized with excess repeat-contiguous DNA with similar kinetics relative to the driver DNA. At completion 80% of that mRNA hybridizable with whole DNA (approximately 65%) had reacted with the repeat-contiguous DNA fraction (50%). This result shows that 80\u2013100% of the mRNA molecules present in sea urchin embryos are transcribed from single copy DNA sequences adjacent to interspersed repetitive sequences in the genome.", "doi": "10.1016/0092-8674(75)90170-1", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1975-03", "series_number": "3", "volume": "4", "issue": "3", "pages": "217-238" }, { "id": "authors:q9ynn-jzb21", "collection": "authors", "collection_id": "q9ynn-jzb21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160812-123233378", "type": "article", "title": "Molecular Aspects of Gene Regulation in Animal Cells", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Gene regulation in animal cells may occur at several stages of RNA metabolism, including synthesis, processing, transport, and utilization of the RNA. This discussion primarily concerns transcription level regulation, i.e., control over which sequences in the genomic DNA are transcribed. Current evidence indicates that this is the initial level of regulation in the differentiated animal cell; this conclusion is supported by quantitative hybridization experiments as well as by other kinds of data. Recent experiments are considered which show that animal structural genes are in general DNA sequences occurring only once per haploid genome. For at least one system, the sea urchin embryo, the amount of nonrepetitive DNA sequence represented in the mRNA's is known. About 14,000 average-sized structural genes are represented in the polysomal mRNA of this 600-cell embryo. Studies on organization of DNA sequences show that at least 80% of the DNA of Xenopus and sea urchin consists of short (300 nucleotides) repetitive sequence elements interspersed with longer nonrepetitive sequence regions. This arrangement is an ordered one, suggesting selective value in evolution and therefore function. Such a sequence arrangement pattern could account for the system properties of gene regulation in animal cells.", "issn": "0008-5472", "publisher": "American Association for Cancer Research", "publication": "Cancer Research", "publication_date": "1974-08", "series_number": "8", "volume": "34", "issue": "8", "pages": "2034-2043" }, { "id": "authors:8stg9-3vj56", "collection": "authors", "collection_id": "8stg9-3vj56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KLEpnas74", "type": "article", "title": "Distribution of repetitive and nonrepetitive sequence transcripts in HeLa mRNA", "author": [ { "family_name": "Klein", "given_name": "William H.", "clpid": "Klein-W-H" }, { "family_name": "Murphy", "given_name": "William", "clpid": "Murphy-W" }, { "family_name": "Attardi", "given_name": "Giuseppe", "clpid": "Attardi-G" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Polyadenylated messenger RNA extracted from HeLa cells was hybridized with a mass excess of HeLa DNA. The kinetics of the hybridization reaction demonstrated that most of the messenger RNA is transcribed from nonrepetitive DNA. The amount of messenger RNA hybridized to DNA was measured both with and without prior RNase treatment. Comparison of the results indicates that within the limits of detection, HeLa messenger RNA does not contain repetitive sequence elements covalently linked to nonrepetitive sequence transcripts. However, a small fraction of the HeLa messenger RNA preparation is transcribed entirely from repetitive DNA sequences. This fraction represents about 6% of the total polyadenylated messenger RNA preparation.", "pmcid": "PMC388325", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1974-05", "series_number": "5", "volume": "71", "issue": "5", "pages": "1785-1789" }, { "id": "authors:1e8zv-45g69", "collection": "authors", "collection_id": "1e8zv-45g69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160811-070814903", "type": "article", "title": "A Measurement of the Sequence Complexity of Polysomal Messenger RNA in Sea Urchin Embryos", "author": [ { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "The first measurement has been made of the number of diverse mRNA sequences (mRNA sequence complexity) in the total polysomes of a eucaryotic system, the sea urchin gastrula. mRNA was purified of nuclear RNA and any other heterogeneous RNA contaminants by release from polysomes with puromycin. Trace quantities of labeled nonrepetitive DNA fragments were hybridized with an excess of mRNA. The hybridization reaction followed ideal first order kinetics in mRNA concentration. At completion of the hybridization reaction, 1.35% of the nonrepetitive DNA was present as mRNA-DNA hybrid. The hybridized DNA was extracted and was at least 70% hybridizable with mRNA, demonstrating a 50-fold purification of the expressed sequences. This purified DNA fraction reassociated with excess unfractionated sea urchin DNA at a rate identical to that of the total nonrepetitive DNA tracer. The mRNA had therefore been hybridized to nonrepetitive DNA sequence, and the amount of hybrid could be used as a direct measure of the mRNA sequence complexity.\nThe complexity of the gastrula mRNA can be calculated as about 17 million nucleotides, sufficient to comprise some 14,000 distinct structural genes. This result also provides an estimate of the number of diverse proteins being translated in the gastrula. From the rate of mRNA-DNA hybrid formation, we estimate that about 8% of the mRNA belongs to this complex class, and that less than 500 copies of each species of message in this class exist per embryo. Most of the mRNA population consists of a relatively small number of diverse species represented a much larger number of times.", "doi": "10.1016/0092-8674(74)90003-8", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1974-05", "series_number": "1", "volume": "2", "issue": "1", "pages": "9-21" }, { "id": "authors:m2xsr-4ey80", "collection": "authors", "collection_id": "m2xsr-4ey80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-121636778", "type": "book_section", "title": "Analysis of repeating DNA sequences by reassociation", "book_title": "Nucleic Acids and Protein Synthesis Part E", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Graham", "given_name": "Dale E.", "clpid": "Graham-D-E" }, { "family_name": "Neufeld", "given_name": "Berney R.", "clpid": "Neufeld-B-R" } ], "contributor": [ { "family_name": "Grossman", "given_name": "Lawrence", "clpid": "Grossman-L" }, { "family_name": "Moldave", "given_name": "Kivie", "clpid": "Moldave-K" } ], "abstract": "Repetitive DNA occurs widely, if not universally, among higher organisms. A variety of procedures has been developed or adapted to examine its characteristics and a body of concepts and language has grown up to deal with its complexities. This chapter attempts to summarize this body of knowledge and technique. Owing to human frailty and the real problems of the subject, it tends to emphasize the approaches and conceptual position. The chapter describes techniques for the analysis of repeating DNA sequences by reassociation and a method for the evaluation of rate constants. The purity of the DNA's used in reassociation is critical, as the presence of contaminating proteins and metal ions can markedly alter reassociation results and reproducibility. Metal ions can be removed from DNA by passing it over Chelex 100 (Bio-Rad Labs) that has been neutralized and equilibrated with buffer.", "doi": "10.1016/0076-6879(74)29033-5", "isbn": "9780121818920", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "1974", "pages": "363-418" }, { "id": "authors:h0nrv-p1479", "collection": "authors", "collection_id": "h0nrv-p1479", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-122552695", "type": "article", "title": "Reduction in the rate of DNA reassociation by sequence divergence", "author": [ { "family_name": "Bonner", "given_name": "Tom I.", "clpid": "Bonner-T-I" }, { "family_name": "Brenner", "given_name": "Don J.", "clpid": "Brenner-D-J" }, { "family_name": "Neufeld", "given_name": "Berney R.", "clpid": "Neufeld-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "An estimate is made of the effect of imperfectly complementary sequences on the rate of reassociation of DNA. Rate measurements are reported for the reassociation of deaminated DNA and for the pairing of DNAs from related bacteria. A method is presented for separating the effect of the incubation temperature on the rate from the effect of sequence divergence. After correction to the optimum incubation temperature, the rate of DNA reassociation appears to be reduced by a factor of two for each 10 deg. C reduction in melting temperature due to sequence divergence. For most typical cases this effect is modest. However it can be quite important for measurements of the relation between the DNAs of different species.", "doi": "10.1016/0022-2836(73)90184-8", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1973-12-05", "series_number": "2", "volume": "81", "issue": "2", "pages": "123-135" }, { "id": "authors:vg8ns-b9592", "collection": "authors", "collection_id": "vg8ns-b9592", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161005-141851183", "type": "article", "title": "Organization, Transcription, and Regulation in the Animal Genome", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "This review concern recent experimental information areas of animal cell molecular biology which are relevant to the mechanism of gene regulation. New data regarding interspersion and clustering of repetitive sequence elements in DNA are considered Molecular characteristics of\nanimal structural genes and mRNAs are discussed, with particular reference the frequency of structural gene sequences, mRNA turn over and the interpretation of dipteran complementation groups. The molecular characteristics of nuclear RNAs, the primary transcription products, are reviewed. Evidence for transcription level regulation is summarized and the relation of nuclear\nand mRNA examined. The protein activator branch of the Britten-Davidson model for gene regulation is further developed and considered in light of current knowledge.", "issn": "0033-5770", "publisher": "University of Chicago Press", "publication": "Quarterly Review of Biology", "publication_date": "1973-12", "series_number": "4", "volume": "48", "issue": "4", "pages": "565-613" }, { "id": "authors:pgvy1-tew66", "collection": "authors", "collection_id": "pgvy1-tew66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GOLpnas73", "type": "article", "title": "Nonrepetitive DNA sequence representation in sea urchin embryo messenger RNA", "author": [ { "family_name": "Goldberg", "given_name": "Robert B.", "clpid": "Goldberg-R-B" }, { "family_name": "Galau", "given_name": "Glenn A.", "clpid": "Galau-G-A" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Messenger RNA was prepared from developing sea urchin gastrulae by puromycin release from polyribosomes. Approximately 60% of the total mRNA radioactivity of the postnuclear supernatant was recovered and shown to be free of any other labeled RNA species such as ribosomal and nuclear RNA. The mRNA was examined by hybridization to DNA present in great excess. The mRNA hybridizes almost exclusively with nonrepetitive DNA. Almost all of the messenger RNA molecules of sea urchin gastrulae therefore consist of transcripts from nonrepetitive sequences. It appears that the structural genes expressed at this stage are typically not repeated in the genome and the mRNA does not include recognizable repetitive sequence.", "pmcid": "PMC427271", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1973-12", "series_number": "12, Pt", "volume": "70", "issue": "12, Pt", "pages": "3516-3520" }, { "id": "authors:52jbg-evn87", "collection": "authors", "collection_id": "52jbg-evn87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160614-165001428", "type": "article", "title": "General interspersion of repetitive with non-repetitive sequence elements in the DNA of Xenopus", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Hough", "given_name": "Barbara R.", "clpid": "Hough-B-R" }, { "family_name": "Amenson", "given_name": "Christopher S.", "clpid": "Amenson-C-S" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The arrangement of repetitive and non-repetitive sequences was studied in the DNA of Xenopus. Labeled DNA sheared to various fragment lengths was reassociated to C_ot 50 (60 \u00b0C, 0.18 m-Na^+) with excess 450 nucleotide fragments of unlabeled DNA, and binding of the labeled DNA to hydroxyapatite was measured. Repetitive sequences monitored in this way are present on about 45% of the 450 nucleotide fragments. As DNA fragment length is increased, larger fractions of the DNA are found to contain repetitive elements. Up to 80% of the DNA binds at an average fragment length of 3700 nueleotides. Analysis of the data shows that a little more than 50% of the genome consists of closely interspersed repetitive and non-repetitive sequences. The average length of the repetitive sequence elements is 300\u00b1100 nueleotides, while the non-repetitive sequences separating adjacent repetitive sequence elements average 800\u00b1200 nueleotides. The remainder of the DNA is mainly non-repetitive, though most of it contains rare interspersed repetitive elements spaced at a minimum of 4000 nueleotides apart. It is concluded that a high degree of order exists in the arrangement of DNA sequences in the Xenopus genome.", "doi": "10.1016/0022-2836(73)90359-8", "issn": "0022-2836", "publisher": "Elsevier", "publication": "Journal of Molecular Biology", "publication_date": "1973-06-15", "series_number": "1", "volume": "77", "issue": "1", "pages": "1-23" }, { "id": "authors:fttvk-v0840", "collection": "authors", "collection_id": "fttvk-v0840", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160802-104636732", "type": "article", "title": "Sequence repetition in the DNA of Nassaria (Ilyanassa) obsoleta", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Hough", "given_name": "Barbara R.", "clpid": "Hough-B-R" }, { "family_name": "Chamberlin", "given_name": "Margaret E.", "clpid": "Chamberlin-M-E" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The reassociation kinetics of the DNA of Ilyanassa obsoleta have been studied in order to obtain a repetition frequency profile for the genome of this organism, a well known subject of embryological interest. At a criterion set about 25\u00b0C below the T_m, Ilyanassa DNA consists of about 38% nonrepetitive sequences; at least 12% of a repetitive sequence component averaging about 20 relatives per sequence; at least 15% of a repetitive sequence component averaging about 1000 relatives per sequence; and 18% of a component which reassociates extremely rapidly and either contains regions of internal homology or consists of a small number of extremely frequent sequences, or both.", "doi": "10.1016/0012-1606(71)90041-8", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "1971-07", "series_number": "3", "volume": "25", "issue": "3", "pages": "445-463" }, { "id": "authors:dgp99-nqc58", "collection": "authors", "collection_id": "dgp99-nqc58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160811-072314286", "type": "article", "title": "Note on the Control of Gene Expression during Development", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The process of development is interpreted in terms of a recent theory of gene regulation. In that theory agents interact with sensor structures associated with the genome. It was proposed that these interactions lead to the transcription of integrator genes and their products in turn effect control of the transcription of many genes and establish patterns of gene activation. The elements of the theory appear sufficient, in principle, to explain the process of development. We assume that there exists an initial divergence in genetic activity due to an unequal distribution of egg cytoplasmic regulatory elements among the different cells in early cleavage. As a result particular sensor structures could be synthesized in some cells and not in others. Therefore, individual cells would differ in their response to external inductive agents arising, for example, in nearby cell layers. Each specific cell or cell type would then be characterized by the integrated activation of a proper set of genes and be capable of carrying out its role in subsequent developmental events.", "doi": "10.1016/0022-5193(71)90140-8", "issn": "0022-5193", "publisher": "Elsevier", "publication": "Journal of Theoretical Biology", "publication_date": "1971-07", "series_number": "1", "volume": "32", "issue": "1", "pages": "123-130" }, { "id": "authors:556ym-a9964", "collection": "authors", "collection_id": "556ym-a9964", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160815-073623366", "type": "article", "title": "Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Recent experimental information on DNA sequence repetition is reviewed, and the significance of both repetitive and non-repetitive sequence considered. Included are a summary of data on the distribution of genome sizes in animals, new experiments on interspecific DNA homology, the distribution of sequence frequencies, and the interspersion of repetitive sequences within the genome. Aspects of the process of evolution are considered at the level of change in the DNA. the process by which novel structure and function could have arisen during evolution are considered speculatively in terms of the authors' gene regulation theory (Britten and Davidson, 1969).", "doi": "10.1086/406830", "issn": "0033-5770", "publisher": "University of Chicago Press", "publication": "Quarterly Review of Biology", "publication_date": "1971-06", "series_number": "2", "volume": "46", "issue": "2", "pages": "111-138" }, { "id": "authors:nn96k-x9b06", "collection": "authors", "collection_id": "nn96k-x9b06", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120725-114721531", "type": "article", "title": "Transcription of Nonrepeated DNA in Neonatal and Fetal Mice", "author": [ { "family_name": "Gelderman", "given_name": "A. H.", "clpid": "Gelderman-A-H" }, { "family_name": "Rake", "given_name": "A. V.", "clpid": "Rake-A-V" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" } ], "abstract": "The transcription of nonrepeated DNA sequences was measured by hybridization of RNA from neonatal and fetal mice to mouse DNA using three different techniques. The measurements indicate that a large part (about 70%) of the rapidly-labeled fetal RNA is transcribed from nonrepeated DNA sequences. It appears that more than 12% of the single-copy DNA sequences are represented in the RNA of newborn mice.", "pmcid": "PMC391189", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1971-01", "series_number": "1", "volume": "68", "issue": "1", "pages": "172-176" }, { "id": "authors:17hw1-13968", "collection": "authors", "collection_id": "17hw1-13968", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160727-100412965", "type": "article", "title": "Gene Regulation for Higher Cells: A Theory", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "Cell differentiation is based almost certainly on the regulation of gene activity, so that for each state of differentiation a certain set of genes is active in transcription and other genes are inactive. The establishment of this concept (1) has depended on evidence\nindicating that the cells of an organism generally contain identical genomes (2). Direct support for the idea that regulation of gene activity underlies cell differentiation\ncomes from evidence that much of the genome in higher cell\ntypes is inactive (3) and that different ribonucleic acids (RNA) are synthesized in different cell types (4).", "doi": "10.1126/science.165.3891.349", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1969-07-25", "series_number": "3891", "volume": "165", "issue": "3891", "pages": "349-357" }, { "id": "authors:bp3f5-hwd95", "collection": "authors", "collection_id": "bp3f5-hwd95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151211-102948468", "type": "article", "title": "Repeated Sequences in DNA", "author": [ { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Kohne", "given_name": "D. E.", "clpid": "Kohne-D-E" } ], "abstract": "Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms.", "doi": "10.1126/science.161.3841.529", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1968-08-09", "series_number": "3841", "volume": "161", "issue": "3841", "pages": "529-540" }, { "id": "authors:s5ngf-v3973", "collection": "authors", "collection_id": "s5ngf-v3973", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160520-142711111", "type": "article", "title": "Nucleotide Sequence Repetition: A Rapidly Reassociating Fraction of Mouse DNA", "author": [ { "family_name": "Waring", "given_name": "Michael", "clpid": "Waring-M" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "The separated complemnentary strands of a minor component in mouse DNA reassociate with each other much more rapidly than do the complementary strands of other DNA's including those of the principal part of mouse DNA. This difference in capacity of the strands to reassociate can be used to effect a preparative separation of the minor component from the principal fraction. The rate constant for reassociation of the minor component, compared with those of viral and bacterial DNA's, indicates that the minor component consists of a short nucleotide sequence present in about one million copies.", "doi": "10.1126/science.154.3750.791", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1966-11-11", "series_number": "3750", "volume": "154", "issue": "3750", "pages": "791-794" }, { "id": "authors:938y4-wcn85", "collection": "authors", "collection_id": "938y4-wcn85", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160520-143106637", "type": "article", "title": "Complementary Strand Association between Nucleic Acids and Nucleic Acid Gels", "author": [ { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" } ], "abstract": "Nucleic acid gels can be formed as a result of the cross-linking action of ultraviolet light or of nitrous acid. Such gels form duplex combinations with complementary nucleic acid strands.", "doi": "10.1126/science.142.3594.963", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1963-11-15", "series_number": "3594", "volume": "142", "issue": "3594", "pages": "963-965" }, { "id": "authors:m7jny-cep98", "collection": "authors", "collection_id": "m7jny-cep98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160727-103724960", "type": "article", "title": "Incorporation of Ribonucleic Acid Bases into the Metabolic Pool and RNA of E. coli", "author": [ { "family_name": "Buchwald", "given_name": "M.", "clpid": "Buchwald-M" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" } ], "abstract": "Labeled cytosine, adenine, and guanine are rapidly incorporated by E. coli. A fraction of the radioactivity passes directly into RNA with very little delay. The remainder enters a pool before being incorporated into RNA. The fractions entering the pool and the time constants for equilibration of the specific activity of the pool are widely different for the four RNA bases.", "doi": "10.1016/S0006-3495(63)86811-3", "pmcid": "PMC1366433", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "1963-03", "series_number": "2", "volume": "3", "issue": "2", "pages": "155-166" }, { "id": "authors:hp39c-fq555", "collection": "authors", "collection_id": "hp39c-fq555", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120920-104129614", "type": "article", "title": "The Amino Acid Pool in Escherichia Coli", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "McClure", "given_name": "F. T.", "clpid": "McClure-F-T" } ], "abstract": "Bacteria maintain internally synthesized small molecules at high internal concentrations and in addition have the capacity to concentrate many compounds from the environment. Since the majority of these compounds are intermediates in synthesis, they are collectively termed the pool of metabolic intermediates or, simply, the \"pool.\" However, the state of organization and ultimate chemical fate of exogenous compounds concentrated by the cell may\nbe different from those of identical compounds\nsynthesized by the cell.", "pmcid": "PMC441154", "issn": "0005-3678", "publisher": "Microbiology and Molecular Biology Reviews", "publication": "Bacteriological Reviews", "publication_date": "1962-09", "series_number": "3", "volume": "26", "issue": "3", "pages": "292-335" }, { "id": "authors:0yww4-gqm05", "collection": "authors", "collection_id": "0yww4-gqm05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160727-133214333", "type": "article", "title": "The Synthesis of Ribosomes in E. coli. III. Synthesis of Ribosomal RNA", "author": [ { "family_name": "McCarthy", "given_name": "B. J.", "clpid": "McCarthy-B-J" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Roberts", "given_name": "R. B.", "clpid": "Roberts-R-B" } ], "abstract": "Techniques of chromatography on columns of DEAE^1 cellulose and sedimentation analysis through a sucrose gradient have been used to study the flow of C^(14)-uracil label through precursors to completed ribosomes. Analysis by chromatography shows the existence of two sequential precursors constituting together some 10 per cent of the total ribosomal RNA. The chromatographic separation into three fractions is ascribed to the lower protein/RNA ratios of the precursor. By sedimentation the primary precursor (eosome) is identified as a component of average sedimentation coefficient 14S. The second precursor stage (neosome) is divided among at least two particles, one of 43S and the other of about 30S. Detailed kinetic analysis shows that all the radioactivity passes through the eosome on its way to finished 50S and 30S ribosomes. The delay in the entry of radioactivity to ribosomes is that expected from the quantity of eosome precursor. The obvious conclusion that there exists a precursor-product relationship is discussed together with possible interpretations.", "doi": "10.1016/S0006-3495(62)86841-6", "pmcid": "PMC1366389", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "1962-01", "series_number": "1", "volume": "2", "issue": "1", "pages": "57-82" }, { "id": "authors:9q41y-9gk88", "collection": "authors", "collection_id": "9q41y-9gk88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160727-134712765", "type": "article", "title": "The Synthesis of Ribosomes in E. coli. I. The Incorporation of C^(14)-Uracil into the Metabolic Pool and RNA", "author": [ { "family_name": "McCarthy", "given_name": "B. J.", "clpid": "McCarthy-B-J" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" } ], "abstract": "C^(14)-uracil is rapidly incorporated by E. coli at low concentrations. Approximately half the radioactivity passes directly into RNA with very little delay. The remaining half enters a large metabolic pool and later is incorporated into RNA. The total rate of uptake (growing cells) is not greater than the requirement for uracil and cytosine for RNA synthesis. The size of the metabolic pool is not influenced measurably by the external uracil concentration. No evidence is found for the existence of a fraction of RNA which is rapidly synthesized and degraded.", "doi": "10.1016/S0006-3495(62)86839-8", "pmcid": "PMC1366387", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "1962-01", "series_number": "1", "volume": "2", "issue": "1", "pages": "35-47" }, { "id": "authors:g2wwy-yd454", "collection": "authors", "collection_id": "g2wwy-yd454", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160727-132635677", "type": "article", "title": "The Synthesis of Ribosomes in E. coli. IV. The Synthesis of Ribosomal Protein and the Assembly of Ribosomes", "author": [ { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "McCarthy", "given_name": "B. J.", "clpid": "McCarthy-B-J" }, { "family_name": "Roberts", "given_name": "R. B.", "clpid": "Roberts-R-B" } ], "abstract": "The incorporation of C^(14) leucine into the protein moiety of ribosomes has been studied as a sequel to the studies of ribosomal RNA synthesis. In contrast to the latter studies, labeled leucine is incorporated directly into 50S and 30S ribosomes without measurable delay by precursor stages. There is, however, evidence of some transfer of radioactivity from the 43S group of particles to the 50S. The inhibition of protein synthesis by chloramphenicol results in the accumulation of material similar to the eosome\u2014the primary precursor in ribosome synthesis. There is also evidence for the synthesis of some neosome. The results of the studies of ribosomal RNA and protein synthesis are combined into a model of ribosome synthesis. Finally, consideration is made of the significance of these studies of ribosome synthesis for general problems of protein synthesis and information transfer.", "doi": "10.1016/S0006-3495(62)86842-8", "pmcid": "PMC1366390", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "1962-01", "series_number": "1", "volume": "2", "issue": "1", "pages": "83-93" }, { "id": "authors:jbb2k-1x332", "collection": "authors", "collection_id": "jbb2k-1x332", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160727-133958870", "type": "article", "title": "The Synthesis of Ribosomes in E. coli. II. Analysis of the Kinetics of Tracer Incorporation in Growing Cells", "author": [ { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "McCarthy", "given_name": "B. J.", "clpid": "McCarthy-B-J" } ], "abstract": "Equations are derived representing the flow of radioactive tracer in a sequence of reactions. The conditions under which the equations are applicable are defined. A function \u03d5, representing the newly synthesized fraction is defined, and its use in the analysis of precursor-product relationships is discussed.", "doi": "10.1016/S0006-3495(62)86840-4", "pmcid": "PMC1366388", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "1962-01", "series_number": "1", "volume": "2", "issue": "1", "pages": "49-55" }, { "id": "authors:bkagj-h8555", "collection": "authors", "collection_id": "bkagj-h8555", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160727-131627307", "type": "article", "title": "A Model for the Mechanism of Enzyme Induction", "author": [ { "family_name": "Roberts", "given_name": "R. B.", "clpid": "Roberts-R-B" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "McClure", "given_name": "F. T.", "clpid": "McClure-F-T" } ], "abstract": "A sequence of reactions is postulated from which are derived equations describing the time course of enzyme induction. The model also yields the observed effect of the inducer concentration on the time constant and final rate of enzyme synthesis. Features of the model are: (a) The inducer acts first to release the protein forming template from its site of synthesis on the gene. (b) The inducer is involved again in the equilibrium dissociation of the free template-inducer complex which is utilized in the synthesis of the enzyme-forming unit. (c) The final enzyme-forming unit is unstable and must be synthesized continuously to maintain enzyme synthesis.", "doi": "10.1016/S0006-3495(61)86914-2", "pmcid": "PMC1366359", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "1961-11", "series_number": "8", "volume": "1", "issue": "8", "pages": "649-656" }, { "id": "authors:zgg3x-ft293", "collection": "authors", "collection_id": "zgg3x-ft293", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160728-081754076", "type": "article", "title": "Sedimentation characteristics of bacterial ribonucleoprotein obtained at different periods during the cell-division cycle", "author": [ { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Lark", "given_name": "K. G.", "clpid": "Lark-K-G" }, { "family_name": "Norcross", "given_name": "F.", "clpid": "Norcross-F" } ], "abstract": "A large proportion of the ribonucleic acid of bacteria occurs in the form of ribonudeoprotein particles. In growing Escherichia coli, these particles (ribosomes) are distributed among a number of different classes having sedimentation coefficients of approximately 20 S, 30 S, 50 S, 70 S and 100 S. The sedimentation coefficient of the\nlargest particle varies between 70 S and 100 S depending on the magnesium concentration. At low concentration (10^(-4) M) the 70-S and 100-S particles, dissociate into 30-S and 50-S particles.", "doi": "10.1016/0006-3002(60)90132-3", "issn": "0006-3002", "publisher": "Elsevier", "publication": "Biochimica et Biophysica Acta", "publication_date": "1960-03-25", "series_number": "1", "volume": "39", "issue": "1", "pages": "150-151" }, { "id": "authors:dmr3h-3f830", "collection": "authors", "collection_id": "dmr3h-3f830", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160520-143415113", "type": "article", "title": "High-Resolution Density Gradient Sedimentation Analysis", "author": [ { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Roberts", "given_name": "R. B.", "clpid": "Roberts-R-B" } ], "abstract": "The principle of stability for a sample layered in a density-gradient liquid column is discussed, and a method for separating ribonucleoprotein particles by means of sedimentation in the ultracentrifuge is described.", "doi": "10.1126/science.131.3392.32", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1960-01-01", "series_number": "3392", "volume": "131", "issue": "3392", "pages": "32-33" }, { "id": "authors:dvewa-6nm67", "collection": "authors", "collection_id": "dvewa-6nm67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MCQpnas59", "type": "article", "title": "Synthesis of nascent protein by ribosomes in Escherichia coli", "author": [ { "family_name": "McQuillen", "given_name": "Kenneth", "clpid": "McQuillen-K" }, { "family_name": "Roberts", "given_name": "Richard B.", "clpid": "Roberts-R-B" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "abstract": "Cells and tissues of all kinds of living organisms have been found to contain ribonucleic acid (RNA) and protein both as separate constituents and as complexes in the form of ribonucleoprotein particles. From a variety of experimental data it has been inferred that these particles are probably intimately involved in the processes of protein synthesis.", "pmcid": "PMC222733", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1959-09", "series_number": "9", "volume": "45", "issue": "9", "pages": "1437-1447" }, { "id": "authors:kgxfc-g4n49", "collection": "authors", "collection_id": "kgxfc-g4n49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BRIpnas55", "type": "article", "title": "Amino acid adsorption and protein synthesis in Escherichia coli", "author": [ { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Roberts", "given_name": "R. B.", "clpid": "Roberts-R-B" }, { "family_name": "French", "given_name": "E. F.", "clpid": "French-E-F" } ], "abstract": "Two quite distinct theories of protein synthesis are currently popular. One holds that amino acids are linked into small peptides which then serve as building blocks for the proteins. The other postulates that amino acids are individually adsorbed on a large template molecule and are then linked together into the polypeptide chains. This paper reports the results of studies of amino acid incorporation by growing Escherichia coli. The results furnish experimental evidence in favor of the template theory.", "pmcid": "PMC534295", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1955-11", "series_number": "11", "volume": "41", "issue": "11", "pages": "863-870" } ]