{"doi":"10.1016/j.jbc.2025.108514","title":"High-frequency transcription leads to rapid R-loop formation","abstract":"R-loops are transcriptionally generated three-stranded nucleic acid structures where the mRNA hybridizes with template DNA, leaving a displaced single-stranded non-template DNA loop. Previously, we demonstrated that R-loop and subsequent G-quadruplex formation upregulate transcription. However, the mechanistic basis of how transcription activity generates R-loop formation is unknown. Here, we investigate the kinetics of transcription and its impact on R-loop formation using single-molecule FRET and EMSA. We show that R-loop formation is tuned by the frequency and the rate of transcription, controlled by the RNA polymerase and NTP concentrations, respectively. We provide a plausible mechanism in which gradually increasing the duration of the promoter opening leads to the R-loop formation. Through stochastic simulation, we demonstrate that the frequency of transcription primarily governs R-loop formation. This work highlights the intricate balance between transcription dynamics and R-loop formation, providing new insights into the structure-function relationship.","journal":"Journal of Biological Chemistry","year":2025,"id":533541,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9502,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1415334,"name":"Chun‐Ying Lee","orcid":"0000-0001-8475-5205","position":1,"is_corresponding":false},{"id":1415761,"name":"Leya Yang","orcid":null,"position":2,"is_corresponding":false},{"id":475672,"name":"Tapas Paul","orcid":"0000-0001-7508-5676","position":3,"is_corresponding":false},{"id":284455,"name":"Sua Myong","orcid":"0000-0001-9098-3423","position":4,"is_corresponding":false},{"id":940293,"name":"Bradleigh E Palmer","orcid":"0000-0001-8694-2522","position":0,"is_corresponding":true}],"reference_count":43,"raw_metadata":null,"created_at":"2026-07-19T02:51:32.301795Z","pmid":"40250562","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":[]}