1. Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH
- Author
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Jacob C. Ulirsch, Masahiro Kanai, Alan Gutierrez, Steven K. Reilly, Kousuke Mouri, Daniel Berenzy, Susan Kales, Ryan Tewhey, Ava Mackay-Smith, Pardis C. Sabeti, Redwan M Bhuiyan, Sager J. Gosai, Michael L. Stitzel, Hilary K. Finucane, Adrianne Gladden-Young, and Gina M Butler
- Subjects
Fatty Acid Desaturases ,Quantitative Trait Loci ,Locus (genetics) ,Computational biology ,Regulatory Sequences, Nucleic Acid ,Biology ,Polymorphism, Single Nucleotide ,Genome ,Article ,Delta-5 Fatty Acid Desaturase ,Proto-Oncogene Proteins ,Genetic variation ,Genetics ,Deoxyribonuclease I ,Humans ,CRISPR ,Gene silencing ,Clustered Regularly Interspaced Short Palindromic Repeats ,GATA1 Transcription Factor ,Epigenetics ,Gene ,In Situ Hybridization, Fluorescence ,Adaptor Proteins, Signal Transducing ,Models, Genetic ,Bayes Theorem ,LIM Domain Proteins ,Flow Cytometry ,K562 Cells ,Function (biology) ,RNA, Guide, Kinetoplastida - 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.
- Published
- 2021
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