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Nat Commun DOI:10.1038/ncomms15403

Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression.

Publication TypeJournal Article
Year of Publication2017
AuthorsRosenbluh, J, Xu, H, Harrington, W, Gill, S, Wang, X, Vazquez, F, Root, DE, Tsherniak, A, Hahn, WC
JournalNat Commun
Date Published2017 May 23

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.


Alternate JournalNat Commun
PubMed ID28534478
PubMed Central IDPMC5457492
Grant ListU01 CA176058 / CA / NCI NIH HHS / United States
U01 CA199253 / CA / NCI NIH HHS / United States