{"doi":"10.1016/j.immuni.2024.02.004","title":"The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling","abstract":"Inducible nucleosome remodeling at hundreds of latent enhancers and several promoters shapes the transcriptional response to Toll-like receptor 4 (TLR4) signaling in macrophages. We aimed to define the identities of the transcription factors that promote TLR-induced remodeling. An analysis strategy based on ATAC-seq and single-cell ATAC-seq that enriched for genomic regions most likely to undergo remodeling revealed that the transcription factor nuclear factor κB (NF-κB) bound to all high-confidence peaks marking remodeling during the primary response to the TLR4 ligand, lipid A. Deletion of NF-κB subunits RelA and c-Rel resulted in the loss of remodeling at high-confidence ATAC-seq peaks, and CRISPR-Cas9 mutagenesis of NF-κB-binding motifs impaired remodeling. Remodeling selectivity at defined regions was conferred by collaboration with other inducible factors, including IRF3- and MAP-kinase-induced factors. Thus, NF-κB is unique among TLR4-activated transcription factors in its broad contribution to inducible nucleosome remodeling, alongside its ability to activate poised enhancers and promoters assembled into open chromatin.","journal":"Immunity","year":2024,"id":417776,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":61,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9586,"is_data_producer":false,"deposit_databanks":null,"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":1204247,"name":"Brandon J. Thomas","orcid":"0000-0002-0983-113X","position":1,"is_corresponding":false},{"id":632803,"name":"Prabhat Kumar Purbey","orcid":"0000-0001-6373-6283","position":2,"is_corresponding":false},{"id":1204248,"name":"Filipe Menegatti de Melo","orcid":"0000-0002-3672-3636","position":3,"is_corresponding":false},{"id":471988,"name":"Xin Liu","orcid":"0000-0003-3256-2940","position":4,"is_corresponding":false},{"id":1177162,"name":"Allison E. Daly","orcid":"0000-0002-7030-8663","position":5,"is_corresponding":false},{"id":68622,"name":"Fei Sun","orcid":"0000-0002-0351-5144","position":6,"is_corresponding":false},{"id":984896,"name":"Jerry Hung-Hao Lo","orcid":null,"position":7,"is_corresponding":false},{"id":871081,"name":"Lijing Cheng","orcid":"0000-0002-9854-0392","position":8,"is_corresponding":false},{"id":37940,"name":"Michael Carey","orcid":"0000-0003-3899-6280","position":9,"is_corresponding":false},{"id":227279,"name":"Philip O. Scumpia","orcid":"0000-0002-2563-2042","position":10,"is_corresponding":false},{"id":254568,"name":"Stephen T. Smale","orcid":"0000-0002-9835-6907","position":11,"is_corresponding":false},{"id":368887,"name":"An‐Chieh Feng","orcid":"0000-0002-0946-8131","position":0,"is_corresponding":true}],"reference_count":64,"raw_metadata":null,"created_at":"2026-07-19T01:56:56.807779Z","pmid":"38430908","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":[]}