{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:21:32Z","timestamp":1792790492960,"version":"4.5.0"},"reference-count":24,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T00:00:00Z","timestamp":1791763200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T00:00:00Z","timestamp":1791763200000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T00:00:00Z","timestamp":1791763200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of General Medical Sciences","award":["R35GM142511"],"award-info":[{"award-number":["R35GM142511"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"crossref"}]},{"award":["R35GM142511"],"award-info":[{"award-number":["R35GM142511"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]},{"name":"W. M. Keck Foundation","award":["1002444"],"award-info":[{"award-number":["1002444"]}],"id":[{"id":"https:\/\/ror.org\/000dswa46","id-type":"ROR","asserted-by":"crossref"}]},{"award":["1002444"],"award-info":[{"award-number":["1002444"]}],"id":[{"id":"https:\/\/ror.org\/000dswa46","id-type":"ROR","asserted-by":"publisher"}]},{"name":"DOD Prostate Cancer Research Program","award":["PC250408"],"award-info":[{"award-number":["PC250408"]}]},{"award":["PC250408"],"award-info":[{"award-number":["PC250408"]}],"id":[{"id":"https:\/\/ror.org\/03df8gj37","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>CRISPR\/Cas9-induced DNA double-strand breaks (DSBs) are widely used for genome engineering, yet their capacity to provoke sister chromatid exchange (SCE) remains incompletely understood because exchanges between identical sisters leave no sequence change and are invisible to conventional sequencing. Using sci-L3-Strand-seq, a scalable single-cell template-strand sequencing platform, we mapped SCE following targeted Cas9 cleavage. Cas9 targeting of a unique genomic locus strongly enriched SCE at the break site, reaching 41% in the same cell cycle and 17% in the subsequent division, indicating frequent non-local inter-sister repair. Targeting 237 repetitive Alu sites produced mild enrichment of on-target SCE, whereas cells with elevated SCE burden showed significant enrichment at programmed cut sites, suggesting context-dependent recombination at repetitive loci. Reciprocal daughter-cell pair analysis revealed large-scale structural alterations on chromosomes with induced SCEs and at SCE junctions, indicating that Cas9-induced SCE does not universally reflect error-free homologous recombination. Disruption of LIG3, LIG4, XRCC1, and XRCC4 at Cas9 cut sites did not measurably alter SCE frequency, consistent with delayed functional loss following editing. Together, these findings identify Cas9-induced DSBs as potent local triggers of SCE and reveal structural outcomes invisible to conventional sequencing.<\/jats:p>","DOI":"10.7554\/elife.112073","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T16:30:10Z","timestamp":1787157010000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.112073","source":"Crossref","is-referenced-by-count":0,"title":["Genome-wide mapping of Cas9-induced sister chromatid exchange across single and over 200 genomic sites in human cells"],"prefix":"10.7554","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8066-1893","authenticated-orcid":true,"given":"Peter","family":"Chovanec","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/046rm7j60","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Human Genetics, David Geffen School of Medicine, UCLA","place":["Los Angeles, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Shiyang","family":"He","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/046rm7j60","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Human Genetics, David Geffen School of Medicine, UCLA","place":["Los Angeles, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0963-2672","authenticated-orcid":true,"given":"Yi","family":"Yin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/046rm7j60","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Human Genetics, David Geffen School of Medicine, UCLA","place":["Los Angeles, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"4374","published-online":{"date-parts":[[2026,10,12]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aeh1834","type":"journal-article","article-title":"A CDK1 phospho-switch reprograms TRAIP to unload replisomes in mitosis","volume":"393","author":"Can","year":"2026","journal-title":"Science"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"7989","DOI":"10.1093\/nar\/gkz487","type":"journal-article","article-title":"Massively parallel profiling and predictive modeling of the outcomes of CRISPR\/Cas9-mediated double-strand break repair","volume":"47","author":"Chen","year":"2019","journal-title":"Nucleic Acids Research"},{"key":"bib3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf101","type":"journal-article","article-title":"Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility","volume":"53","author":"Chovanec","year":"2025","journal-title":"Nucleic Acids Research"},{"key":"bib4","doi-asserted-by":"publisher","DOI":"10.64898\/2026.05.11.724412","type":"preprint","article-title":"Lesions initiating spontaneous mitotic crossover are minimally subject to non-homologous end joining","volume-title":"bioRxiv","author":"Chovanec","year":"2026"},{"key":"bib5","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkag119","type":"journal-article","article-title":"High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq","volume":"54","author":"Chovanec","year":"2026","journal-title":"Nucleic Acids Research"},{"key":"bib6","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1126\/science.1231143","type":"journal-article","article-title":"Multiplex genome engineering using CRISPR\/Cas systems","volume":"339","author":"Cong","year":"2013","journal-title":"Science"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1016\/j.molcel.2018.12.021","type":"journal-article","article-title":"Mitotic CDK promotes replisome disassembly, fork breakage, and complex DNA rearrangements","volume":"73","author":"Deng","year":"2019","journal-title":"Molecular Cell"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1038\/nmeth.2206","type":"journal-article","article-title":"DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution","volume":"9","author":"Falconer","year":"2012","journal-title":"Nature Methods"},{"key":"bib9","doi-asserted-by":"publisher","DOI":"10.1126\/science.aeh2300","type":"journal-article","article-title":"TTF2 processes sites of incomplete DNA replication during mitosis via sister-chromatid exchanges","volume":"393","author":"Fujisawa","year":"2026","journal-title":"Science"},{"key":"bib10","doi-asserted-by":"publisher","DOI":"10.1016\/j.crmeth.2021.100150","type":"journal-article","article-title":"Construction of Strand-seq libraries in open nanoliter arrays","volume":"2","author":"Hanlon","year":"2022","journal-title":"Cell Reports Methods"},{"key":"bib11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34519-8","type":"journal-article","article-title":"Sister chromatid exchanges induced by perturbed replication can form independently of BRCA1, BRCA2 and RAD51","volume":"13","author":"Heijink","year":"2022","journal-title":"Nature Communications"},{"key":"bib12","doi-asserted-by":"publisher","first-page":"5653","DOI":"10.1016\/j.cell.2021.10.002","type":"journal-article","article-title":"Mapping the genetic landscape of DNA double-strand break repair","volume":"184","author":"Hussmann","year":"2021","journal-title":"Cell"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1038\/nbt.4192","type":"journal-article","article-title":"Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements","volume":"36","author":"Kosicki","year":"2018","journal-title":"Nature Biotechnology"},{"key":"bib14","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1038\/s41588-021-00838-7","type":"journal-article","article-title":"Chromothripsis as an on-target consequence of CRISPR-Cas9 genome editing","volume":"53","author":"Leibowitz","year":"2021","journal-title":"Nature Genetics"},{"key":"bib15","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1038\/nbt.2675","type":"journal-article","article-title":"CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering","volume":"31","author":"Mali","year":"2013","journal-title":"Nature Biotechnology"},{"key":"bib16","doi-asserted-by":"publisher","first-page":"1380","DOI":"10.1016\/j.cell.2013.08.021","type":"journal-article","article-title":"Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity","volume":"154","author":"Ran","year":"2013","journal-title":"Cell"},{"key":"bib17","doi-asserted-by":"publisher","first-page":"4119","DOI":"10.1016\/j.molcel.2025.10.015","type":"journal-article","article-title":"Megabase-scale loss of heterozygosity provoked by CRISPR-Cas9 DNA double-strand breaks","volume":"85","author":"Regan","year":"2025","journal-title":"Molecular Cell"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/nbt.3481","type":"journal-article","article-title":"Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA","volume":"34","author":"Richardson","year":"2016","journal-title":"Nature Biotechnology"},{"key":"bib19","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1038\/s41586-018-0686-x","type":"journal-article","article-title":"Predictable and precise template-free CRISPR editing of pathogenic variants","volume":"563","author":"Shen","year":"2018","journal-title":"Nature"},{"key":"bib20","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.48686","type":"journal-article","article-title":"TRAIP drives replisome disassembly and mitotic DNA repair synthesis at sites of incomplete DNA replication","volume":"8","author":"Sonneville","year":"2019","journal-title":"eLife"},{"key":"bib21","doi-asserted-by":"publisher","first-page":"6787","DOI":"10.1093\/nar\/gkw422","type":"journal-article","article-title":"Bromodeoxyuridine does not contribute to sister chromatid exchange events in normal or Bloom syndrome cells","volume":"44","author":"van Wietmarschen","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"bib22","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02760-1","type":"journal-article","article-title":"BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes","volume":"9","author":"van Wietmarschen","year":"2018","journal-title":"Nature Communications"},{"key":"bib23","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1016\/j.cell.2020.10.025","type":"journal-article","article-title":"Allele-specific chromosome removal after cas9 cleavage in human embryos","volume":"183","author":"Zuccaro","year":"2020","journal-title":"Cell"},{"key":"dataset1","type":"dataset","article-title":"Genome-wide mapping of Cas9-induced sister chromatid exchange across single and over 200 genomic targets","volume-title":"NCBI BioProject","author":"Yin","year":"2026","unstructured":"Yin Y. 2026. Genome-wide mapping of Cas9-induced sister chromatid exchange across single and over 200 genomic targets. NCBI BioProject. https:\/\/www.ncbi.nlm.nih.gov\/bioproject\/?term=PRJNA1466603. PRJNA1466603."}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/112073\/elife-112073-v1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/112073\/elife-112073-v1.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/112073","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T11:05:38Z","timestamp":1791803138000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/112073"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,12]]},"references-count":24,"alternative-id":["10.7554\/eLife.112073"],"URL":"https:\/\/doi.org\/10.7554\/elife.112073","archive":["CLOCKSS"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.64898\/2026.05.13.724813","asserted-by":"subject"}],"is-same-as":[{"id-type":"doi","id":"10.7554\/eLife.112073.3","asserted-by":"subject"}],"is-version-of":[{"id-type":"doi","id":"10.7554\/eLife.112073.1","asserted-by":"subject"},{"id-type":"doi","id":"10.7554\/eLife.112073.2","asserted-by":"subject"}],"is-supplemented-by":[{"id-type":"accession","id":"PRJNA1466603","asserted-by":"subject"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,12]]},"assertion":[{"value":"single anonymised","name":"peer_review_transparency","label":"Peer review transparency","group":{"name":"peer_review_taxonomy"}},{"value":"other reviewer(s), editor","name":"peer_review_interaction","label":"Peer review interaction","group":{"name":"peer_review_taxonomy"}},{"value":"review summaries, review reports, author\/editor communication, reviewer identities reviewer opt in, editor identities","name":"peer_review_published","label":"Peer review published","group":{"name":"peer_review_taxonomy"}},{"value":"open (sign in with ORCID iD required)","name":"post_publication_commenting","label":"Post publication commenting","group":{"name":"post_publication_commenting"}}],"article-number":"RP112073"}}