Abstract
Noncoding regulatory elements control gene expression and govern all biological processes. Epigenomic profiling assays have identified millions of putative regulatory elements, but systematically determining the function of each of those regulatory elements remains a substantial challenge. Here we adapt CRISPR-dCas9-based epigenomic regulatory element screening (CERES) technology to screen all >100,000 putative non-coding regulatory elements defined by open chromatin sites in human K562 leukemia cells for their role in regulating essential cellular processes. In an initial screen containing more than 1 million gRNAs, we discovered approximately 12,000 regulatory elements with evidence of impact on cell fitness. We validated many of the screen hits in K562 cells, evaluated cell-type specificity in a second cancer cell line, and identified target genes of regulatory elements using CERES perturbations combined with single cell RNA-seq. This comprehensive and quantitative genome-wide map of essential regulatory elements represents a framework for extensive characterization of noncoding regulatory elements that drive complex cell phenotypes and for prioritizing non-coding genetic variants that likely contribute to common traits and disease risk.
Competing Interest Statement
T.S.K., G.E.C., T.E.R., and C.A.G. are co-founders of Element Genomics. C.A.G. is a co-founder of Tune Therapeutics and Locus Biosciences and is an advisor to Tune Therapeutics, Sarepta Therapeutics, Levo Therapeutics, and Iveric Bio. T.S.K. is a co-founder and employee of Tune Therapeutics. T.S.K., S.S.A., N.I., T.E.R., G.E.C., and C.A.G. are inventors on patents or patent applications related to CRISPR epigenome editing and screening technologies.