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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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.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics Investigative techniques and equipment organism description > bacteria Investigative techniques and equipment > CRISPR-Cas9 |
| CSHL Authors: | |
| Communities: | CSHL Cancer Center Program CSHL Cancer Center Program > Cancer Genetics and Genomics Program CSHL labs > Vakoc lab CSHL Post Doctoral Fellows |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 5 May 2022 |
| Date Deposited: | 17 May 2022 14:20 |
| Last Modified: | 01 Dec 2025 20:14 |
| PMCID: | PMC9072436 |
| URI: | https://repository.cshl.edu/id/eprint/40608 |
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