{"doi":"10.1101/2023.09.24.559224","title":"Analyzing the link between RNA secondary structures and R-loop formation with tree polynomials","abstract":"Abstract R-loops are a class of non-canonical nucleic acid structures that typically form during transcription when the nascent RNA hybridizes the DNA template strand, leaving the DNA coding strand unpaired. Co-transcriptional R-loops are abundant in nature and biologically relevant. Recent research shows that DNA sequence and topology affect R-loops, yet it remains unclear how these and other factors drive R-loop formation. In this work, we investigate a link between the secondary structure of the nascent RNA and the probability of R-loop formation. We introduce tree-polynomial representations, a class of mathematical objects that enable accurate and efficient data analysis of RNA secondary structures. With tree-polynomials, we establish a strong correlation between the secondary structure of the RNA transcript and the probability of R-loop formation. We identify that branches with short stems separated by multiple ‘bubbles’ in the RNA secondary structure are associated with the strong correlation and are predictive of R-loop formation.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":411841,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9488,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1192841,"name":"Jacob Lusk","orcid":null,"position":1,"is_corresponding":false},{"id":1192842,"name":"Nataša Jonoska","orcid":null,"position":2,"is_corresponding":false},{"id":1103273,"name":"Mariel Vázquez","orcid":"0000-0001-8328-6806","position":3,"is_corresponding":false},{"id":1192439,"name":"Pengyu Liu","orcid":"0000-0001-7154-7546","position":0,"is_corresponding":true}],"reference_count":33,"raw_metadata":null,"created_at":"2026-07-19T01:21:46.548301Z","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":[]}