Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH.
Nat Genet 2021 Aug; 53(8):1166-1176
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, Steven K; Gosai, Sager J; Gutierrez, Alan; Mackay-Smith, Ava; Ulirsch, Jacob C; Kanai, Masahiro; Mouri, Kousuke; Berenzy, Daniel; Kales, Susan; Butler, Gina M; Gladden-Young, Adrianne; Bhuiyan, Redwan M; Stitzel, Michael L.; Finucane, Hilary K; Sabeti, Pardis C; and Tewhey, Ryan, "Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH." (2021). Faculty Research 2021. 183.