Effective interpretation of genome function and genetic variation requires a shift from epigenetic mapping of cis-regulatory elements (CREs) to characterization of endogenous function. We developed hybridization chain reaction fluorescence in situ hybridization coupled with flow cytometry (HCR–FlowFISH), a broadly applicable approach to characterize CRISPR-perturbed CREs via accurate quantification of native transcripts, alongside CRISPR activity screen analysis (CASA), a hierarchical Bayesian model to quantify CRE activity. Across >325,000 perturbations, we provide evidence that CREs can regulate multiple genes, skip over the nearest gene and display activating and/or silencing effects. At the cholesterol-level-associated FADS locus, we combine endogenous screens with reporter assays to exhaustively characterize multiple genome-wide association signals, functionally nominate causal variants and, importantly, identify their target genes.
Reilly SK,
Gosai SJ,
Gutierrez A,
Ava Mackay-Smith,
Ulirsch JC,
Kanai M,
Mouri K,
Berenzy D,
Kales S,
Butler GM,
Gladden-Young A,
Bhuiyan RM,
Stitzel ML,
Finucane HK,
Sabeti PC,
Tewhey R
