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.
Deplancke
Bart
B
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA.
Mukhopadhyay
Arnab
A
Ao
Wanyuan
W
Elewa
Ahmed M
AM
Grove
Christian A
CA
Martinez
Natalia J
NJ
Sequerra
Reynaldo
R
Doucette-Stamm
Lynn
L
Reece-Hoyes
John S
JS
Hope
Ian A
IA
Tissenbaum
Heidi A
HA
Mango
Susan E
SE
Walhout
Albertha J M
AJ
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology; D018509:DNA, Helminth / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D004064:Digestive System / Q000378:metabolism; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional; D012441:Saccharomyces cerevisiae / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D020798:Two-Hybrid System Techniques
D029742:Caenorhabditis elegans Proteins; D018509:DNA, Helminth; D004268:DNA-Binding Proteins; D014157:Transcription Factors