Title

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.

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