{"doi":"10.1093/nar/gkae706","title":"Rapid profiling of transcription factor–cofactor interaction networks reveals principles of epigenetic regulation","abstract":"Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here, we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced histone 3 lysine 27 acetylation (H3K27ac). Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data support clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.","journal":"Nucleic Acids Research","year":2024,"id":435689,"datarank":0.4261492982589569,"base_score":2.5649493574615367,"endowment":2.5649493574615367,"self_citation_contribution":0.38474240361923057,"citation_network_contribution":0.04140689463972635,"self_endowment_contribution":0.38474240361923057,"citer_contribution":0.04140689463972635,"corpus_percentile":null,"corpus_rank":null,"citation_count":12,"citer_count":11,"citers_with_citation_signal":6,"citers_with_endowment":6,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9616,"is_data_producer":true,"deposit_databanks":{"figshare":["10.6084/m9.figshare.26364901"],"GEO":["GSE266127"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1243776,"name":"Rebekah Miller","orcid":null,"position":1,"is_corresponding":false},{"id":575128,"name":"Heather Hook","orcid":null,"position":2,"is_corresponding":false},{"id":574413,"name":"David A. Bray","orcid":"0009-0008-7453-3818","position":3,"is_corresponding":false},{"id":574414,"name":"Jessica L. Keenan","orcid":"0000-0001-5012-662X","position":4,"is_corresponding":false},{"id":575129,"name":"Rose Zhao","orcid":null,"position":5,"is_corresponding":false},{"id":680449,"name":"Thomas D. Gilmore","orcid":"0000-0002-1910-768X","position":6,"is_corresponding":false},{"id":56375,"name":"Trevor Siggers","orcid":"0000-0002-8039-7639","position":7,"is_corresponding":false},{"id":1243286,"name":"Melissa M Inge","orcid":"0000-0001-7654-8994","position":0,"is_corresponding":true}],"reference_count":124,"raw_metadata":null,"created_at":"2026-07-19T02:00:08.103086Z","pmid":"39166482","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}