RT Journal
A1 Kudron, Michelle
A1 Gevirtzman, Louis
A1 Victorsen, Alec
A1 Lear, Bridget C.
A1 Gao, Jiahao
A1 Xu, Jinrui
A1 Samanta, Swapna
A1 Frink, Emily
A1 Tran-Pearson, Adri
A1 Huynh, Chau
A1 Vafeados, Dionne
A1 Hammonds, Ann
A1 Fisher, William
A1 Wall, Martha
A1 Wesseling, Greg
A1 Hernandez, Vanessa
A1 Lin, Zhichun
A1 Kasparian, Mary
A1 White, Kevin
A1 Allada, Ravi
A1 Gerstein, Mark
A1 Hillier, LaDeana
A1 Celniker, Susan E.
A1 Reinke, Valerie
A1 Waterston, Robert H.
T1 Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
JF Genome Research 
JO Genome Research 
YR 2024 
FD December 01 
VO 34 
IS 12 
SP 2319 
OP 2334 
DO 10.1101/gr.279037.124 
UL http://genome.cshlp.org/content/34/12/2319.abstract 
AB A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.