title: Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.
abstract: Regulation of gene expression by sequence-specific transcription factors is central to developmental programs and depends on the binding of transcription factors with target sites in the genome. To date, most such analyses in Caenorhabditis elegans have focused on the interactions between a single transcription factor with one or a few select target genes. As part of the modENCODE Consortium, we have used chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) to determine the genome-wide binding sites of 22 transcription factors (ALR-1, BLMP-1, CEH-14, CEH-30, EGL-27, EGL-5, ELT-3, EOR-1, GEI-11, HLH-1, LIN-11, LIN-13, LIN-15B, LIN-39, MAB-5, MDL-1, MEP-1, PES-1, PHA-4, PQM-1, SKN-1, and UNC-130) at diverse developmental stages. For each factor we determined candidate gene targets, both coding and non-coding. The typical binding sites of almost all factors are within a few hundred nucleotides of the transcript start site. Most factors target a mixture of coding and non-coding target genes, although one factor preferentially binds to non-coding RNA genes. We built a regulatory network among the 22 factors to determine their functional relationships to each other and found that some factors appear to act preferentially as regulators and others as target genes. Examination of the binding targets of three related HOX factors--LIN-39, MAB-5, and EGL-5--indicates that these factors regulate genes involved in cellular migration, neuronal function, and vulval differentiation, consistent with their known roles in these developmental processes. Ultimately, the comprehensive mapping of transcription factor binding sites will identify features of transcriptional networks that regulate C. elegans developmental processes.
authors.affiliation: Department of Genetics, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Niu
authors.forename: Zhi John
authors.initials: ZJ
authors.lastname: Lu
authors.forename: Mei
authors.initials: M
authors.lastname: Zhong
authors.forename: Mihail
authors.initials: M
authors.lastname: Sarov
authors.forename: John I
authors.initials: JI
authors.lastname: Murray
authors.forename: Cathleen M
authors.initials: CM
authors.lastname: Brdlik
authors.forename: Judith
authors.initials: J
authors.lastname: Janette
authors.forename: Chao
authors.initials: C
authors.lastname: Chen
authors.forename: Pedro
authors.initials: P
authors.lastname: Alves
authors.forename: Elicia
authors.initials: E
authors.lastname: Preston
authors.forename: Cindie
authors.initials: C
authors.lastname: Slightham
authors.forename: Lixia
authors.initials: L
authors.lastname: Jiang
authors.forename: Anthony A
authors.initials: AA
authors.lastname: Hyman
authors.forename: Stuart K
authors.initials: SK
authors.lastname: Kim
authors.forename: Robert H
authors.initials: RH
authors.lastname: Waterston
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Valerie
authors.initials: V
authors.lastname: Reinke
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D017173:Caenorhabditis elegans / Q000166:cytology / Q000235:genetics* / Q000378:metabolism*; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D022661:RNA, Untranslated / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D024363:Transcription Initiation Site
chemical_list: D022661:RNA, Untranslated; D014157:Transcription Factors