A gene-centered C. elegans protein-DNA interaction network
Graduate School of Biomedical Sciences; Program in Gene Function and Expression; Program in Molecular Medicine
Medical Subject Headings
Animals; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Computational Biology; DNA, Helminth; DNA-Binding Proteins; Digestive System; Promoter Regions (Genetics); Regulatory Elements, Transcriptional; Saccharomyces cerevisiae; Transcription Factors; Transcription, Genetic; Two-Hybrid System Techniques
Life Sciences | Medicine and Health Sciences
Transcription regulatory networks consist of physical and functional interactions between transcription factors (TFs) and their target genes. The systematic mapping of TF-target gene interactions has been pioneered in unicellular systems, using "TF-centered" methods (e.g., chromatin immunoprecipitation). However, metazoan systems are less amenable to such methods. Here, we used "gene-centered" high-throughput yeast one-hybrid (Y1H) assays to identify 283 interactions between 72 C. elegans digestive tract gene promoters and 117 proteins. The resulting protein-DNA interaction (PDI) network is highly connected and enriched for TFs that are expressed in the digestive tract. We provide functional annotations for approximately 10% of all worm TFs, many of which were previously uncharacterized, and find ten novel putative TFs, illustrating the power of a gene-centered approach. We provide additional in vivo evidence for multiple PDIs and illustrate how the PDI network provides insights into metazoan differential gene expression at a systems level.
Y1H dataset can be found as a supplemental file to this paper. See Additional Files below. Legend at bottom of Excel spreadsheet.
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Citation: Cell. 2006 Jun 16;125(6):1193-205. Link to article on publisher's site