{"doi":"10.1101/2022.07.07.499190","title":"RNA polymerase II and PARP1 shape enhancer-promoter contacts","abstract":"Abstract How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we studied enhancer-promoter contact architecture and communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription, and perturbations to transcription-associated proteins and thousands of candidate enhancers. Contact frequency between functionally validated enhancer-promoter pairs was most enriched near the +1 and +2 nucleosomes at enhancers and target promoters, indicating that functional enhancer-promoter pairs spend time in close physical proximity. Blocking RNA polymerase II (Pol II) caused major disruptions to enhancer-promoter contacts. Paused Pol II occupancy and the enzymatic activity of poly (ADP-ribose) polymerase 1 (PARP1) stabilized enhancer-promoter contacts. Based on our findings, we propose an updated model that couples transcriptional dynamics and enhancer-promoter communication.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":297542,"datarank":0.6938225541917061,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.3484347902425992,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.3484347902425992,"corpus_percentile":null,"corpus_rank":null,"citation_count":9,"citer_count":9,"citers_with_citation_signal":9,"citers_with_endowment":9,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9492,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":397185,"name":"James J. Lewis","orcid":"0000-0002-4170-9118","position":1,"is_corresponding":false},{"id":560245,"name":"Alexandra G. Chivu","orcid":"0000-0001-8875-3530","position":2,"is_corresponding":false},{"id":689754,"name":"Abderhman Abuhashem","orcid":"0000-0002-6135-5679","position":3,"is_corresponding":false},{"id":68355,"name":"Nils Krietenstein","orcid":"0000-0003-2519-6305","position":4,"is_corresponding":false},{"id":551441,"name":"Edward J. Rice","orcid":null,"position":5,"is_corresponding":false},{"id":37164,"name":"Oliver J. Rando","orcid":"0000-0003-1516-9397","position":6,"is_corresponding":false},{"id":255184,"name":"Anna‐Katerina Hadjantonakis","orcid":"0000-0002-7580-5124","position":7,"is_corresponding":false},{"id":19579,"name":"Charles G. Danko","orcid":"0000-0002-1999-7125","position":8,"is_corresponding":false},{"id":575647,"name":"Gilad Barshad","orcid":"0000-0001-7845-7658","position":0,"is_corresponding":true}],"reference_count":92,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:31:26.161109Z","pmid":null,"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":[]}