@book_section {CaltechAUTHORS_https://authors.library.caltech.edu/id/eprint/42373,
    title ="A Framework for piRNA Cluster Manipulation",
    author = "Olovnikov, Ivan and Le Thomas, Adrien",
    
    
    number = "1093",
    pages = "47-58",
    month = "January",
    year = "2014",
    doi = "10.1007/978-1-62703-694-8_5",
    
    isbn = "978-1-62703-693-1",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20131112-093205322",
    note = "© 2014 Springer Science+Business Media, LLC. We thank members of the Aravin lab for helpful discussion and\ncomments on the manuscript. We are particularly thankful to\nAlexandre Webster for comments and editing. I.O. is a CEMI\n(Center for Environmental Microbiology Interactions) fellow at\nCaltech. This work was supported by grants from the National\nInstitutes of Health (R01 GM097363, R00 HD057233, and DP2\nOD007371A) and the Searle Scholar Award to A.A.A.",
    revision_no = "13",
    abstract = "Piwi proteins and their small-RNA partners, piwi-interacting (pi)RNA, form a natural mechanism that\nprevents the deleterious activity of transposable elements in the germ line of metazoan species. The piRNA pathway relies on extended noncoding genomic regions, dubbed piRNA clusters, to produce long precursor transcripts that are subsequently processed into mature piRNAs. The large size and repetitive nature of piRNA clusters provide significant challenges for their dissection using common genetic tools. Here we describe an effective approach for manipulation of piRNA clusters using a combination of BAC recombineering\nin E. coli and phiC31-mediated transgenesis in Drosophila. Although the described approach is instrumental for manipulating piRNA clusters, it can also be implemented for other problems in functional genomics.",
}
@book_section {CaltechAUTHORS_https://authors.library.caltech.edu/id/eprint/95361,
    title ="Analysis of Large-Scale Sequencing of Small RNAs",
    author = "Olson, A. J. and Brennecke, J.",
    
    
    
    pages = "126-136",
    month = "January",
    year = "2008",
    doi = "10.1142/9789812776136_0014",
    
    isbn = "9789812776082",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190509-081714112",
    note = "© 2008 World Scientific Publishing Company. \n\nThe authors acknowledge the help of Ted Roeder and Ankit Patel with various aspects of the front end for the web-based software and the anonymous reviewers for suggesting numerous improvements to the manuscript.",
    revision_no = "11",
    abstract = "The advent of large-scale sequencing has opened up new areas of research, such as the study of Piwi-interacting small RNAs (piRNAs). piRNAs are longer than miRNAs, close to 30 nucleotides in length, involved in various functions, such as the suppression of transposons in germline 3,4,5. Since a large number of them (many tens of thousands) are generated from a wide range of positions in the genome, large-scale sequencing is the only way to study them. The key to understanding their genesis and biological roles is efficient analysis, which is complicated by the large volumes of sequence data. Taking account of the underlying biology is also important. We describe here novel analyses techniques and tools applied to small RNAs from germ cells in D. melanogaster, that allowed us to infer mechanism and biological function.",
}
@book_section {CaltechAUTHORS_https://authors.library.caltech.edu/id/eprint/95359,
    title ="Small RNA Silencing Pathways in Germ and Stem Cells",
    author = "Aravin, A. A. and Hannon, G. J.",
    journal = "Cold Spring Harbor Symposia on Quantitative Biology",
    
    number = "73",
    pages = "283-290",
    month = "January",
    year = "2008",
    doi = "10.1101/sqb.2008.73.058",
    issn = "0091-7451",
    isbn = "978-087969862-1",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190509-074849509",
    note = "© 2008 Cold Spring Harbor Laboratory Press. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). \n\nWe thank members of the Hannon lab for helpful discussions. This work was supported by grants from the National Institutes of Health (NIH) to G.J.H. and an NIH Pathway to Independence Award K99HD057233 to A.A.A.",
    revision_no = "10",
    abstract = "During the past several years, it has become clear that small RNAs guard germ cell genomes from the activity of mobile genetic elements. Indeed, in mammals, a class of small RNAs, known as Piwi-interacting RNAs (piRNAs), forms an innate immune system that discriminates transposons from endogenous genes and selectively silences the former. piRNAs enforce silencing by directing transposon DNA methylation during male germ cell development. As such, piRNAs represent perhaps the only currently known sequence-specific factor for deposition of methylcytosine in mammals. The three mammalian Piwi proteins Miwi2, Mili, and Miwi are required at different stages of germ cell development. Moreover, distinct classes of piRNAs are expressed in developmental waves, with particular generative loci and different sequence content distinguishing piRNAs populations in embryonic germ cells from those that appear during meiosis. Although our understanding of Piwi proteins and piRNA biology have deepened substantially during the last several years, major gaps still exist in our understanding of these enigmatic RNA species.",
}