Comparative optimization of combinatorial CRISPR screens

Li, Ruitong, Klingbeil, Olaf, Monducci, Davide, Young, Michael J, Rodriguez, Diego J, Bayyat, Zaid, Dempster, Joshua M, Kesar, Devishi, Yang, Xiaoping, Zamanighomi, Mahdi, Vakoc, Christopher R, Ito, Takahiro, Sellers, William R (May 2022) Comparative optimization of combinatorial CRISPR screens. Nature Communications, 13 (1). p. 2469. ISSN 2041-1723

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DOI: 10.1038/s41467-022-30196-9


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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
Investigative techniques and equipment > CRISPR-Cas9
CSHL Authors:
Communities: CSHL labs > Vakoc lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 5 May 2022
Date Deposited: 17 May 2022 14:20
Last Modified: 17 May 2022 14:20
PMCID: PMC9072436

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