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Comparative optimization of combinatorial CRISPR screens.

ABSTRACT: Combinatorial CRISPR technologies have emerged as a transformative approach to systematically probe genetic interactions and dependencies of redundant gene pairs. However, the performance of different functional genomic tools for multiplexing sgRNAs vary widely. Here, we generate and benchmark ten distinct pooled combinatorial CRISPR libraries targeting paralog pairs to optimize digenic knockout screens. Libraries composed of dual Streptococcus pyogenes Cas9 (spCas9), orthogonal spCas9 and Staphylococcus aureus (saCas9), and enhanced Cas12a from Acidaminococcus were evaluated. We demonstrate a combination of alternative tracrRNA sequences from spCas9 consistently show superior effect size and positional balance between the sgRNAs as a robust combinatorial approach to profile genetic interactions of multiple genes.

SUBMITTER: Li R

PROVIDER: S-EPMC9072436 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Comparative optimization of combinatorial CRISPR screens.

Li Ruitong R Klingbeil Olaf O Monducci Davide D Young Michael J MJ Rodriguez Diego J DJ Bayyat Zaid Z Dempster Joshua M JM Kesar Devishi D Yang Xiaoping X Zamanighomi Mahdi M Vakoc Christopher R CR Ito Takahiro T Sellers William R WR

Nature communications 20220505 1

Combinatorial CRISPR technologies have emerged as a transformative approach to systematically probe genetic interactions and dependencies of redundant gene pairs. However, the performance of different functional genomic tools for multiplexing sgRNAs vary widely. Here, we generate and benchmark ten distinct pooled combinatorial CRISPR libraries targeting paralog pairs to optimize digenic knockout screens. Libraries composed of dual Streptococcus pyogenes Cas9 (spCas9), orthogonal spCas9 and Staph ...[more]

PMID: 35513429

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