CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein coding elements in the genome as a having a central role in various biological processes. However, decoding the function of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR–Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR–Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity within the native genomic context. Using dCas9(KRAB) repressor and dCas9(p300) activator constructs and lentiviral sgRNA libraries targeting DNase I hypersensitive sites surrounding a gene of interest, we perform both loss- and gain-of-function screens to identify regulatory elements for the β-globin and the HER2 loci in human cells. CERES readily identified known and novel regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context.