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Target-enriched nan...
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Geng, KYKarolinska Institutet
(author)
Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
- Article/chapterEnglish2022
Publisher, publication year, extent ...
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2022-09-30
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Cold Spring Harbor Laboratory,2022
Numbers
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LIBRIS-ID:oai:prod.swepub.kib.ki.se:151647724
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http://kipublications.ki.se/Default.aspx?queryparsed=id:151647724URI
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https://doi.org/10.1101/gr.276901.122DOI
Supplementary language notes
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Language:English
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Summary in:English
Part of subdatabase
Classification
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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The CRISPR-Cas9 system is widely used to permanently delete genomic regions via dual guide RNAs. Genomic rearrangements induced by CRISPR-Cas9 can occur, but continuous technical developments make it possible to characterize complex on-target effects. We combined an innovative droplet-based target enrichment approach with long-read sequencing and coupled it to a customized de novo sequence assembly. This approach enabled us to dissect the sequence content at kilobase scale within an on-target genomic locus. We here describe extensive genomic disruptions by Cas9, involving the allelic co-occurrence of a genomic duplication and inversion of the target region, as well as integrations of exogenous DNA and clustered interchromosomal DNA fragment rearrangements. Furthermore, we found that these genomic alterations led to functional aberrant DNA fragments and can alter cell proliferation. Our findings broaden the consequential spectrum of the Cas9 deletion system, reinforce the necessity of meticulous genomic validations, and introduce a data-driven workflow enabling detailed dissection of the on-target sequence content with superior resolution.
Added entries (persons, corporate bodies, meetings, titles ...)
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Merino, LGKarolinska Institutet
(author)
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Wedemann, L
(author)
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Martens, A
(author)
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Sobota, M
(author)
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Sanchez, YPKarolinska Institutet
(author)
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Sondergaard, JN
(author)
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White, RJ
(author)
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Kutter, CKarolinska Institutet
(author)
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Karolinska Institutet
(creator_code:org_t)
Related titles
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In:Genome research: Cold Spring Harbor Laboratory32:10, s. 1876-18911549-54691088-9051
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