Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH.
Nat Genet
; 53(8): 1166-1176, 2021 08.
Article
in En
| MEDLINE
| ID: mdl-34326544
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.
Full text:
1
Database:
MEDLINE
Main subject:
Regulatory Sequences, Nucleic Acid
/
In Situ Hybridization, Fluorescence
Type of study:
Prognostic_studies
/
Risk_factors_studies
Limits:
Humans
Language:
En
Year:
2021
Type:
Article