Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH.
Document Type
Article
Publication Date
8-2021
Publication Title
Nature genetics
Keywords
JGM, JMG
JAX Source
Nat Genet 2021 Aug; 53(8):1166-1176
Volume
53
Issue
8
First Page
1166
Last Page
1176
ISSN
1546-1718
PMID
34326544
DOI
https://doi.org/10.1038/s41588-021-00900-4
Grant
HG008179
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 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.
Recommended Citation
Reilly S,
Gosai S,
Gutierrez A,
Mackay-Smith A,
Ulirsch J,
Kanai M,
Mouri K,
Berenzy D,
Kales S,
Butler G,
Gladden-Young A,
Bhuiyan R,
Stitzel ML,
Finucane H,
Sabeti P,
Tewhey R.
Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH. Nat Genet 2021 Aug; 53(8):1166-1176