title: Genomic cis-regulatory networks in the early Ciona intestinalis embryo.
abstract: Precise spatiotemporal gene expression during animal development is achieved through gene regulatory networks, in which sequence-specific transcription factors (TFs) bind to cis-regulatory elements of target genes. Although numerous cis-regulatory elements have been identified in a variety of systems, their global architecture in the gene networks that regulate animal development is not well understood. Here, we determined the structure of the core networks at the cis-regulatory level in early embryos of the chordate Ciona intestinalis by chromatin immunoprecipitation (ChIP) of 11 TFs. The regulatory systems of the 11 TF genes examined were tightly interconnected with one another. By combining analysis of the ChIP data with the results of previous comprehensive analyses of expression profiles and knockdown of regulatory genes, we found that most of the previously determined interactions are direct. We focused on cis-regulatory networks responsible for the Ciona mesodermal tissues by examining how the networks specify these tissues at the level of their cis-regulatory architecture. We also found many interactions that had not been predicted by simple gene knockdown experiments, and we showed that a significant fraction of TF-DNA interactions make major contributions to the regulatory control of target gene expression.
authors.affiliation: Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kubo
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Suzuki
authors.forename: Xuyang
authors.initials: X
authors.lastname: Yuan
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakai
authors.forename: Nori
authors.initials: N
authors.lastname: Satoh
authors.forename: Kaoru S
authors.initials: KS
authors.lastname: Imai
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Satou
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D019521:Body Patterning / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D002938:Ciona intestinalis / Q000196:embryology* / Q000235:genetics*; D004625:Embryo, Nonmammalian; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks / Q000502:physiology*; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis; D011485:Protein Binding / Q000502:physiology; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics / Q000502:physiology*; D013997:Time Factors; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors