We describe a combinatorial CRISPR interference (CRISPRi) screening platform for mapping genetic interactions in mammalian cells. We targeted 107 chromatin-regulation factors in human cells with pools of either single or double single guide RNAs (sgRNAs) to downregulate individual genes or gene pairs, respectively. Relative enrichment analysis of individual sgRNAs or sgRNA pairs allowed for quantitative characterization of genetic interactions, and comparison with protein–protein-interaction data revealed a functional map of chromatin regulation.
The authors thank the members of the laboratories of L.S.Q. and N.J.K. for advice and helpful discussions, and the Stanford Functional Genomics Facility and UCSD Sequencing Facility for technical support. We thank D. Zhao from the laboratory of L.S.Q. for advice and help in cloning the sgRNA library. L.S.Q. acknowledges support from the NIH Office of the Director (OD), the National Institute of Dental & Craniofacial Research (NIDCR), the Department of Defense Breast Cancer Research Breakthrough Program, the Pew Charitable Trusts and the Alfred P. Sloan Foundation. D.D. and A.R. acknowledge support from the Quantitative Bioscience Institute (QBI). M.C., N.J.K. and L.S.Q. acknowledge support from the J. David Gladstone Biofulcrum Program. This work was supported by DP5 OD017887, NIH R01 DA036858, NIH U01EB021240, DOD W81XWH-17-1-0018, a Pew Scholar Fellowship and an Alfred P. Sloan Fellowship to L.S.Q., as well as by NIH grants P50 GM082250, U19 AI106754, P01 HL089707, R01 GM084279, U19 AI118610 and R01 AI120694 to N.J.K.
Double sgRNA screens raw data and data used in individual figures