| 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
|
| Resource |
| C.elegans |
tm1542
tm4401
tm1787
tm1375
tm455
tm321
tm1336
tm6453 |
