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.

对基因组功能和遗传变异的有效解释需要从顺式调控元件（CRE）的表观遗传图谱转向内源功能的表征。我们开发了杂交链式反应荧光原位杂交与流式细胞术 (HCR-FlowFISH) 的结合，这是一种广泛适用的方法，可通过准确定量天然转录本来表征 CRISPR 扰动的 CRE，同时还开发了 CRISPR 活性筛选分析 (CASA)，这是一种分层贝叶斯模型，用于分析受 CRISPR 干扰的 CRE。量化 CRE 活动。在 >325,000 个扰动中，我们提供的证据表明 CRE 可以调节多个基因、跳过最近的基因并显示激活和/或沉默效果。在与胆固醇水平相关的FADS位点，我们将内源性筛选与报告基因检测相结合，以详尽地表征多个全基因组关联信号，在功能上指定因果变异，并且重要的是，识别其目标基因。