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Enabling large-scale genome editing at repetitive elements by reducing DNA nicking.

ABSTRACT: To extend the frontier of genome editing and enable editing of repetitive elements of mammalian genomes, we made use of a set of dead-Cas9 base editor (dBE) variants that allow editing at tens of thousands of loci per cell by overcoming the cell death associated with DNA double-strand breaks and single-strand breaks. We used a set of gRNAs targeting repetitive elements-ranging in target copy number from about 32 to 161 000 per cell. dBEs enabled survival after large-scale base editing, allowing targeted mutations at up to ?13 200 and ?12 200 loci in 293T and human induced pluripotent stem cells (hiPSCs), respectively, three orders of magnitude greater than previously recorded. These dBEs can overcome current on-target mutation and toxicity barriers that prevent cell survival after large-scale genome engineering.

SUBMITTER: Smith CJ

PROVIDER: S-EPMC7229841 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Enabling large-scale genome editing at repetitive elements by reducing DNA nicking.

Smith Cory J CJ Castanon Oscar O Said Khaled K Volf Verena V Khoshakhlagh Parastoo P Hornick Amanda A Ferreira Raphael R Wu Chun-Ting CT Güell Marc M Garg Shilpa S Ng Alex H M AHM Myllykallio Hannu H Church George M GM

Nucleic acids research 20200501 9

To extend the frontier of genome editing and enable editing of repetitive elements of mammalian genomes, we made use of a set of dead-Cas9 base editor (dBE) variants that allow editing at tens of thousands of loci per cell by overcoming the cell death associated with DNA double-strand breaks and single-strand breaks. We used a set of gRNAs targeting repetitive elements-ranging in target copy number from about 32 to 161 000 per cell. dBEs enabled survival after large-scale base editing, allowing ...[more]

PMID: 32315033

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