title: The comprehensive transcriptional analysis in Caenorhabditis elegans by integrating ChIP-seq and gene expression data.
abstract: The fundamental step of learning transcriptional regulation mechanism is to identify the target genes regulated by transcription factors (TFs). Despite numerous target genes identified by chromatin immunoprecipitation followed by high-throughput sequencing technology (ChIP-seq) assays, it is not possible to infer function from binding alone in vivo. This is equally true in one of the best model systems, the nematode Caenorhabditis elegans (C. elegans), where regulation often occurs through diverse TF binding features of transcriptional networks identified in modENCODE. Here, we integrated ten ChIP-seq datasets with genome-wide expression data derived from tiling arrays, involved in six TFs (HLH-1, ELT-3, PQM-1, SKN-1, CEH-14 and LIN-11) with tissue-specific and four TFs (CEH-30, LIN-13, LIN-15B and MEP-1) with broad expression patterns. In common, TF bindings within 3 kb upstream of or within its target gene for these ten studies showed significantly elevated level of expression as opposed to that of non-target controls, indicated that these sites may be more likely to be functional through up-regulating its target genes. Intriguingly, expression of the target genes out of 5 kb upstream of their transcription start site also showed high levels, which was consistent with the results of following network component analysis. Our study has identified similar transcriptional regulation mechanisms of tissue-specific or broad expression TFs in C. elegans using ChIP-seq and gene expression data. It may also provide a novel insight into the mechanism of transcriptional regulation not only for simple organisms but also for more complex species.
authors.affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences,Anhui University, Hefei City,People's Republic of China.
authors.forename: Kan
authors.initials: K
authors.lastname: He
authors.affiliation: Department of Biology,Hong Kong Baptist University,Hong Kong,China.
authors.forename: Jiaofang
authors.initials: J
authors.lastname: Shao
authors.affiliation: Department of Biology,Hong Kong Baptist University,Hong Kong,China.
authors.forename: Zhongying
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences,Anhui University, Hefei City,People's Republic of China.
authors.forename: Dahai
authors.initials: D
authors.lastname: Liu
mesh_terms: D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics* / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D029742:Caenorhabditis elegans Proteins; D014157:Transcription Factors