Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH

被引：42

作者：

Reilly, Steven K. ^{[1
,2
]}

Gosai, Sager J. ^{[1
,2
,3
]}

Gutierrez, Alan ^{[1
]}

Mackay-Smith, Ava ^{[1
]}

Ulirsch, Jacob C. ^{[1
,3
,4
]}

Kanai, Masahiro ^{[1
,4
,5
]}

Mouri, Kousuke ^{[6
]}

Berenzy, Daniel ^{[6
]}

Kales, Susan ^{[6
]}

Butler, Gina M. ^{[1
]}

Gladden-Young, Adrianne ^{[1
]}

Bhuiyan, Redwan M. ^{[7
,8
]}

Stitzel, Michael L. ^{[7
,8
,9
]}

Finucane, Hilary K. ^{[1
,4
]}

Sabeti, Pardis C. ^{[1
,2
,10
,11
]}

Tewhey, Ryan ^{[6
,12
,13
]}

机构：

[1] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[2] Harvard Univ, Ctr Syst Biol, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA

[3] Harvard Grad Program Biol & Biomed Sci, Boston, MA USA

[4] Massachusetts Gen Hosp, Analyt & Translat Genet Unit, Boston, MA 02114 USA

[5] Harvard Med Sch, Program Bioinformat & Integrat Genom, Boston, MA 02115 USA

[6] Jackson Lab, 600 Main St, Bar Harbor, ME 04609 USA

[7] Jackson Lab Genom Med, Farmington, CT USA

[8] Univ Connecticut, Dept Genet & Genome Sci, Farmington, CT USA

[9] Univ Connecticut, Inst Syst Genom, Farmington, CT USA

[10] Howard Hughes Med Inst, Chevy Chase, MD 20815 USA

[11] Harvard TH Chan Sch Publ Hlth, Dept Immunol & Infect Dis, Boston, MA 02115 USA

[12] Univ Maine, Grad Sch Biomed Sci & Engn, Orono, ME 04469 USA

[13] Tufts Univ, Sch Med, Grad Sch Biomed Sci, Boston, MA 02111 USA

来源：

NATURE GENETICS | 2021年 / 53卷 / 08期

关键词：

DNA ELEMENTS; CELL; TRANSCRIPTION; EXPRESSION; PROMOTER; SINGLE; IDENTIFICATION; INTERROGATION; ENCYCLOPEDIA; SELECTION;

D O I：

10.1038/s41588-021-00900-4

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

HCR-FlowFISH is a new approach to characterize CRISPR-perturbed cis-regulatory elements (CREs) via accurate quantification of native transcripts, alongside CRISPR activity screen analysis (CASA), a hierarchical Bayesian model to quantify CRE activity. 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.

引用

页码：1166 / +

页数：22

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