A gene-centered C. elegans protein-DNA interaction network
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.
Keywords: Animals ; Caenorhabditis elegans/genetics/metabolism ; Caenorhabditis elegans Proteins/genetics/metabolism ; Computational Biology ; DNA ; Helminth/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Digestive System/metabolism ; Promoter Regions (Genetics) ; Regulatory Elements ; Transcriptional ; Saccharomyces cerevisiae/genetics ; Transcription Factors/metabolism ; Transcription ; Genetic ; Two-Hybrid System Techniques
Previewed in: Cell, 125(6):1032-4, 2006
Record created on 2008-07-15, modified on 2016-08-08