[ { "id": "authors:zjpr0-9cn52", "collection": "authors", "collection_id": "zjpr0-9cn52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170418-093907798", "type": "article", "title": "Sequential Response to Multiple Developmental Network Circuits Encoded in an Intronic cis- Regulatory Module of Sea Urchin hox11/13b", "author": [ { "family_name": "Cui", "given_name": "Miao", "clpid": "Cui-Miao" }, { "family_name": "Vielmas", "given_name": "Erika", "clpid": "Vielmas-E" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Peter", "given_name": "Isabelle S.", "orcid": "0000-0003-3685-3147", "clpid": "Peter-I-S" } ], "abstract": "Gene expression in different spatial domains is often controlled by separate cis-regulatory modules (CRMs), but regulatory states determining CRM activity are not only distinct in space, they also change continuously during developmental time. Here, we systematically analyzed the regulatory sequences controlling hox11/13b expression and identified a single CRM required throughout embryonic gut development. We show that within this CRM, distinct sets of binding sites recognizing Ets, Tcf, and homeodomain transcription factors control the dynamic spatial expression of hox11/13b in each developmental phase. Several binding sites execute multiple, sometimes contradictory, regulatory functions, depending on the temporal and spatial regulatory context. In addition, we identified a nearby second CRM operating in inter-modular AND logic with the first CRM to control hox11/13b expression in hindgut endoderm. Our results suggest a mechanism for continuous gene expression in response to changing developmental network functions that depends on sequential combinatorial regulation of individual CRMs.", "doi": "10.1016/j.celrep.2017.03.039", "issn": "2211-1247", "publisher": "Elsevier", "publication": "Cell Reports", "publication_date": "2017-04-11", "series_number": "2", "volume": "19", "issue": "2", "pages": "364-374" }, { "id": "authors:1se4h-fb726", "collection": "authors", "collection_id": "1se4h-fb726", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141111-151009684", "type": "article", "title": "Specific functions of the Wnt signaling system in gene regulatory networks throughout the early sea urchin embryo", "author": [ { "family_name": "Cui", "given_name": "Miao", "clpid": "Cui-Miao" }, { "family_name": "Siriwon", "given_name": "Natnaree", "clpid": "Siriwon-N" }, { "family_name": "Li", "given_name": "Enhu", "clpid": "Li-Enhu" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Peter", "given_name": "Isabelle S.", "orcid": "0000-0003-3685-3147", "clpid": "Peter-I-S" } ], "abstract": "Wnt signaling affects cell-fate specification processes throughout embryonic development. Here we take advantage of the well-studied gene regulatory networks (GRNs) that control pregastrular sea urchin embryogenesis to reveal the gene regulatory functions of the entire Wnt-signaling system. Five wnt genes, three frizzled genes, two secreted frizzled-related protein 1 genes, and two Dickkopf genes are expressed in dynamic spatial patterns in the pregastrular embryo of Strongylocentrotus purpuratus. We present a comprehensive analysis of these genes in each embryonic domain. Total functions of the Wnt-signaling system in regulatory gene expression throughout the embryo were studied by use of the Porcupine inhibitor C59, which interferes with zygotic Wnt ligand secretion. Morpholino-mediated knockdown of each expressed Wnt ligand demonstrated that individual Wnt ligands are functionally distinct, despite their partially overlapping spatial expression. They target specific embryonic domains and affect particular regulatory genes. The sum of the effects of blocking expression of individual wnt genes is shown to equal C59 effects. Remarkably, zygotic Wnt-signaling inputs are required for only three general aspects of embryonic specification: the broad activation of endodermal GRNs, the regional specification of the immediately adjacent stripe of ectoderm, and the restriction of the apical neurogenic domain. All Wnt signaling in this pregastrular embryo is short range (and/or autocrine). Furthermore, we show that the transcriptional drivers of wnt genes execute important specification functions in the embryonic domains targeted by the ligands, thus connecting the expression and function of wnt genes by encoded cross-regulatory interactions within the specific regional GRNs.", "doi": "10.1073/pnas.1419141111", "pmcid": "PMC4250154", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2014-11-25", "series_number": "47", "volume": "111", "issue": "47", "pages": "E5029-E5038" }, { "id": "authors:8krj7-gnd46", "collection": "authors", "collection_id": "8krj7-gnd46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140225-091728610", "type": "article", "title": "Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo", "author": [ { "family_name": "Li", "given_name": "Enhu", "clpid": "Li-Enhu" }, { "family_name": "Cui", "given_name": "Miao", "clpid": "Cui-Miao" }, { "family_name": "Peter", "given_name": "Isabelle S.", "orcid": "0000-0003-3685-3147", "clpid": "Peter-I-S" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "abstract": "By gastrulation the ectodermal territories of the sea urchin embryo have developed an unexpectedly complex spatial pattern of sharply bounded regulatory states, organized orthogonally with respect to the animal/vegetal and oral/aboral axes of the embryo. Although much is known of the gene regulatory network (GRN) linkages that generate these regulatory states, the principles by which the boundaries between them are positioned and maintained have remained undiscovered. Here we determine the encoded genomic logic responsible for the boundaries of the oral aspect of the embryo that separate endoderm from ectoderm and ectoderm from neurogenic apical plate and that delineate the several further subdivisions into which the oral ectoderm per se is partitioned. Comprehensive regulatory state maps, including all spatially expressed oral ectoderm regulatory genes, were established. The circuitry at each boundary deploys specific repressors of regulatory states across the boundary, identified in this work, plus activation by broadly expressed positive regulators. These network linkages are integrated with previously established interactions on the oral/aboral axis to generate a GRN model encompassing the 2D organization of the regulatory state pattern in the pregastrular oral ectoderm of the embryo.", "doi": "10.1073/pnas.1323105111", "pmcid": "PMC3956148", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2014-03-11", "series_number": "10", "volume": "111", "issue": "10", "pages": "E906-E913" } ]