Gene regulatory networks, comprising interactions between transcription factors (TFs) and regulatory DNA regions, play critical roles in development, physiology and responses to environmental cues. In recent years, chromatin immunoprecipitation (ChIP) assays greatly expanded our view of the genomic regions occupied by individual TFs. However, only ~10% of the ~900 C. elegans TFs have been assayed by ChIP. Here, we use gene-centered enhanced yeast one-hybrid (eY1H) assays to identify 21,679 protein-DNA interactions between 366 C. elegans TFs and 2,576 promoters. By integrating this network with co-expression data, we characterize TFs as transcriptional activators or repressors. We identify new targets for previously characterized TFs that we further validated by qPCR in TF mutants strains. Additionally, we predict the function of uncharacterized TFs by evaluating interactions with targets associated with specific gene ontology terms. For instance, we identify a module of nuclear hormone receptors that bind to the promoters of detoxifying enzymes. Altogether, this large-scale dataset provides a blueprint to study TF and target gene functions.
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