RT Journal
A1 Niu, Wei
A1 Lu, Zhi John
A1 Zhong, Mei
A1 Sarov, Mihail
A1 Murray, John I.
A1 Brdlik, Cathleen M.
A1 Janette, Judith
A1 Chen, Chao
A1 Alves, Pedro
A1 Preston, Elicia
A1 Slightham, Cindie
A1 Jiang, Lixia
A1 Hyman, Anthony A.
A1 Kim, Stuart K.
A1 Waterston, Robert H.
A1 Gerstein, Mark
A1 Snyder, Michael
A1 Reinke, Valerie
T1 Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
JF Genome Research 
JO Genome Research 
YR 2011 
FD February 01 
VO 21 
IS 2 
SP 245 
OP 254 
DO 10.1101/gr.114587.110 
UL http://genome.cshlp.org/content/21/2/245.abstract 
AB 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.