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          Institute: MPI für molekulare Zellbiologie und Genetik     Collection: Publikationen MPI-CBG 2011-arch     Display Documents



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ID: 585243.0, MPI für molekulare Zellbiologie und Genetik / Publikationen MPI-CBG 2011-arch
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.
Authors:Niu, Wei; Lu, Zhi John; Zhong, Mei; Sarov, Mihail; Murray, James T; Brdlik, Cathleen M; Janette, Judith; Chen, Chao; Alves, Pedro; Preston, Elicia A.; Slightam, Cindie; Jiang, Lixia; Hyman, Anthony A.; Kim, Stuart K; Waterston, Robert H; Gerstein, Mark; Snyder, Michael; Reinke, Valerie
Date of Publication (YYYY-MM-DD):2011
Title of Journal:Genome Research
Volume:21
Issue / Number:2
Start Page:245
End Page:254
Copyright:not available
Audience:Experts Only
Intended Educational Use:No
Abstract / Description: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.
External Publication Status:published
Document Type:Article
Version Comment:Automatic journal name synchronization
Communicated by:thuem
Affiliations:MPI für molekulare Zellbiologie und Genetik
Identifiers:LOCALID:4333
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