Open AccessDirect characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH
Author(s) -
Steven K. Reilly,
Sager J. Gosai,
Alan Gutierrez,
Ava Mackay-Smith,
Jacob C. Ulirsch,
Masahiro Kanai,
Kousuke Mouri,
Daniel Berenzy,
Susan Kales,
Gina M Butler,
Adrianne Gladden-Young,
Redwan M Bhuiyan,
Michael L. Stitzel,
Hilary Finucane,
Pardis C. Sabeti,
R Tewhey
Publication year - 2021
Publication title -
nature genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 18.861
H-Index - 573
eISSN - 1546-1718
pISSN - 1061-4036
DOI - 10.1038/s41588-021-00900-4
Subject(s) - biology , genetics , computational biology , gene , locus (genetics) , epigenetics , genome , gene silencing , function (biology)
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.