{"doi":"10.1016/j.xgen.2023.100291","title":"Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements","abstract":"Diverse inbred mouse strains are important biomedical research models, yet genome characterization of many strains is fundamentally lacking in comparison with humans. In particular, catalogs of structural variants (SVs) (variants ≥ 50 bp) are incomplete, limiting the discovery of causative alleles for phenotypic variation. Here, we resolve genome-wide SVs in 20 genetically distinct inbred mice with long-read sequencing. We report 413,758 site-specific SVs affecting 13% (356 Mbp) of the mouse reference assembly, including 510 previously unannotated coding variants. We substantially improve the Mus musculus transposable element (TE) callset, and we find that TEs comprise 39% of SVs and account for 75% of altered bases. We further utilize this callset to investigate how TE heterogeneity affects mouse embryonic stem cells and find multiple TE classes that influence chromatin accessibility. Our work provides a comprehensive analysis of SVs found in diverse mouse genomes and illustrates the role of TEs in epigenetic differences.","journal":"Cell Genomics","year":2023,"id":317742,"datarank":0.6456097639806255,"base_score":4.304065093204169,"endowment":4.304065093204169,"self_citation_contribution":0.6456097639806255,"citation_network_contribution":0.0,"self_endowment_contribution":0.6456097639806255,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":73,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.5164,"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":19694,"name":"Peter A. Audano","orcid":"0000-0002-5187-0415","position":1,"is_corresponding":false},{"id":19711,"name":"Parithi Balachandran","orcid":"0000-0003-3256-1403","position":2,"is_corresponding":false},{"id":318618,"name":"Anne Czechanski","orcid":"0000-0003-3210-4210","position":3,"is_corresponding":false},{"id":848446,"name":"Jacob I. Flores","orcid":"0000-0001-8863-091X","position":4,"is_corresponding":false},{"id":833167,"name":"Alexander A. Radecki","orcid":"0000-0001-6615-9960","position":5,"is_corresponding":false},{"id":984861,"name":"Varun Mosur","orcid":null,"position":6,"is_corresponding":false},{"id":246456,"name":"David Gordon","orcid":"0000-0001-6552-4022","position":7,"is_corresponding":false},{"id":299621,"name":"Isha A. Walawalkar","orcid":"0000-0002-9152-6651","position":8,"is_corresponding":false},{"id":2125,"name":"Evan E. Eichler","orcid":"0000-0002-8246-4014","position":9,"is_corresponding":false},{"id":275075,"name":"Laura G. Reinholdt","orcid":"0000-0003-4054-4048","position":10,"is_corresponding":false},{"id":19742,"name":"Christine R. Beck","orcid":"0000-0001-7821-8489","position":11,"is_corresponding":false},{"id":984154,"name":"Ardian Ferraj","orcid":"0000-0001-5155-4693","position":0,"is_corresponding":true}],"reference_count":108,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:06:55.884740Z","pmid":"37228752","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":[]}