Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression

Joseph Rosenbluh, Han Xu, William Harrington, Stanley Gill, Xiaoxing Wang, Francisca Vazquez, David E. Root, Aviad Tsherniak and William C. Hahn ()
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Joseph Rosenbluh: Broad Institute of Harvard and MIT
Han Xu: Broad Institute of Harvard and MIT
William Harrington: Broad Institute of Harvard and MIT
Stanley Gill: Broad Institute of Harvard and MIT
Xiaoxing Wang: Broad Institute of Harvard and MIT
Francisca Vazquez: Broad Institute of Harvard and MIT
David E. Root: Broad Institute of Harvard and MIT
Aviad Tsherniak: Broad Institute of Harvard and MIT
William C. Hahn: Broad Institute of Harvard and MIT

Nature Communications, 2017, vol. 8, issue 1, 1-8

Abstract: Abstract CRISPR-Cas9 provides the means to perform genome editing and facilitates loss-of-function screens. However, we and others demonstrated that expression of the Cas9 endonuclease induces a gene-independent response that correlates with the number of target sequences in the genome. An alternative approach to suppressing gene expression is to block transcription using a catalytically inactive Cas9 (dCas9). Here we directly compare genome editing by CRISPR-Cas9 (cutting, CRISPRc) and gene suppression using KRAB-dCas9 (CRISPRi) in loss-of-function screens to identify cell essential genes. CRISPRc identified 98% of previously defined cell essential genes. After optimizing library construction by analysing transcriptional start sites (TSS), CRISRPi identified 92% of core cell essential genes and did not show a bias to regions involved in copy number alterations. However, bidirectional promoters scored as false positives in CRISRPi. We conclude that CRISPRc and CRISPRi have different off-target effects and combining these approaches provides complementary information in loss-of-function genetic screens.

Date: 2017
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DOI: 10.1038/ncomms15403

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