{"doi":"10.1101/2024.05.07.592855","title":"AAV-mediated genome editing is influenced by the formation of R-loops","abstract":"Recombinant adeno-associated viral vectors (rAAV) hold an intrinsic ability to stimulate homologous recombination (AAV-HR) and are the most used in clinical settings for in vivo gene therapy. However, rAAVs also integrate throughout the genome. Here, we describe DNA-RNA immunoprecipitation sequencing (DRIP-seq) in murine HEPA1-6 hepatoma cells and whole murine liver to establish the similarities and differences in genomic R-loop formation in a transformed cell line and intact tissue. We show enhanced AAV-HR in mice upon genetic and pharmacological upregulation of R-loops. Selecting the highly expressed Albumin gene as a model locus for genome editing in both in vitro and in vivo experiments showed that the R-loop prone, 3’ end of Albumin was efficiently edited by AAV-HR, whereas the upstream R-loop- deficient region did not result in detectable vector integration. In addition, we found a positive correlation between previously reported off-target rAAV integration sites and R-loop enriched genomic regions. Thus, we conclude that high levels of R-loops, present in highly transcribed genes, promote rAAV vector genome integration. These findings may shed light on potential mechanisms for improving the safety and efficacy of genome editing by modulating R-loops and may enhance our ability to predict regions most susceptible to off-target insertional mutagenesis by rAAV vectors.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":497475,"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":0.9563,"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":282444,"name":"Magdalena P. Crossley","orcid":"0000-0002-8509-4645","position":1,"is_corresponding":false},{"id":584859,"name":"Aranyak Goswami","orcid":"0000-0001-5368-5371","position":2,"is_corresponding":false},{"id":248365,"name":"Feijie Zhang","orcid":null,"position":3,"is_corresponding":false},{"id":395839,"name":"Katja Pekrun","orcid":"0000-0001-8346-1889","position":4,"is_corresponding":false},{"id":584561,"name":"Jada L. Garzon","orcid":"0000-0003-0389-6108","position":5,"is_corresponding":false},{"id":92045,"name":"Karlene A. Cimprich","orcid":"0000-0002-1937-2969","position":6,"is_corresponding":false},{"id":245569,"name":"Mark A. Kay","orcid":"0000-0002-2799-2615","position":7,"is_corresponding":false},{"id":424604,"name":"Francesco Puzzo","orcid":"0000-0001-9936-8873","position":0,"is_corresponding":true}],"reference_count":69,"raw_metadata":null,"created_at":"2026-07-19T02:09:34.764412Z","pmid":"38766176","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":[]}