RRC ID 53351
Author Fuxman Bass JI, Pons C, Kozlowski L, Reece-Hoyes JS, Shrestha S, Holdorf AD, Mori A, Myers CL, Walhout AJ.
Title A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions.
Journal Mol Syst Biol
Abstract Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein-DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized ~10% of TFs in any metazoan species. The nematode C. elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences. Here, we delineated the largest gene-centered metazoan PDI network to date by examining interactions between 90% of C. elegans TFs and 15% of gene promoters. We used this network as a backbone to predict TF binding sites for 77 TFs, two-thirds of which are novel, as well as integrate gene expression, protein-protein interaction, and phenotypic data to predict regulatory and biological functions for multiple genes and TFs.
Volume 12(10)
Pages 884
Published 2016-10-24
DOI 10.15252/msb.20167131
PMID 27777270
PMC PMC5081483
MeSH Animals Binding Sites Caenorhabditis elegans / chemistry Caenorhabditis elegans / genetics* Caenorhabditis elegans / metabolism Caenorhabditis elegans Proteins / chemistry Caenorhabditis elegans Proteins / metabolism Gene Expression Regulation Protein Binding Protein Interaction Maps RNA, Messenger / chemistry RNA, Messenger / metabolism* RNA, Protozoan / metabolism Transcription Factors / chemistry Transcription Factors / metabolism*
IF 8.991
Times Cited 18
C.elegans tm1542 tm4401 tm1787 tm1375 tm455 tm321 tm1336 tm6453