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Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH

Steven K Reilly, Sager J Gosai, Alan Gutierrez, Ava Mackay-Smith, Jacob C Ulirsch, Masahiro Kanai, Kousuke Mouri, Daniel Berenzy, Susan Kales, Gina B Butler, Adrianne Gladden-Young, Michael L Stitzel, Hilary K Finucane, Pardis C Sabeti, Ryan Tewhey.
Nature Genetics. 2021-07-29;53:1166-1176.
Abstract
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 HCR-FlowFISH, a broadly applicable approach to characterize CRISPR-perturbed CREs via accurate quantification of native transcripts, alongside CASA (CRISPR Activity Screen Analysis), 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 can 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 nominating causal variants and importantly, identifying their target genes.