CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants

被引：7

作者：

Bray, David ^{[1
,2
,3
]}

Hook, Heather ^{[1
,2
]}

Zhao, Rose ^{[1
,2
]}

Keenan, Jessica L. ^{[1
,2
,3
]}

Penvose, Ashley ^{[1
,2
]}

Osayame, Yemi ^{[1
,2
]}

Mohaghegh, Nima ^{[1
,2
]}

Chen, Xiaoting ^{[4
]}

Parameswaran, Sreeja ^{[4
]}

Kottyan, Leah C. ^{[4
,8
]}

Weirauch, Matthew T. ^{[4
,5
,6
,7
]}

Siggers, Trevor ^{[1
,2
]}

机构：

[1] Boston Univ, Dept Biol, Boston, MA 02215 USA

[2] Boston Univ, Biol Design Ctr, Boston, MA 02215 USA

[3] Boston Univ, Bioinformat Program, Boston, MA USA

[4] Cincinnati Childrens Hosp Med Ctr, Ctr Autoimmune Genom & Etiol, Cincinnati, OH USA

[5] Cincinnati Childrens Hosp Med Ctr, Div Dev Biol, Cincinnati, OH USA

[6] Cincinnati Childrens Hosp Med Ctr, Div Biomed Informat, Cincinnati, OH USA

[7] Univ Cincinnati, Coll Med, Dept Pediat, Cincinnati, OH USA

[8] Cincinnati Childrens Hosp Med Ctr, Div Allergy & Immunol, Cincinnati, OH 45229 USA

来源：

CELL GENOMICS | 2022年 / 2卷 / 02期

基金：

美国国家卫生研究院;

关键词：

TRANSCRIPTION-FACTOR-BINDING; GENE-EXPRESSION; IFN-GAMMA; R PACKAGE; PROTEIN; SINGLE; SPECIFICITY; MICROARRAYS; ASSOCIATION; RECEPTORS;

D O I：

10.1016/j.xgen.2022.100098

中图分类号：

Q2 [细胞生物学];

学科分类号：

071009 ; 090102 ;

摘要：

Non-coding DNA variants (NCVs) impact gene expression by altering binding sites for regulatory complexes. New high-throughput methods are needed to characterize the impact of NCVs on regulatory complexes. We developed CASCADE (Customizable Approach to Survey Complex Assembly at DNA Elements), an array based high-throughput method to profile cofactor (COF) recruitment. CASCADE identifies DNA-bound transcription factor-cofactor (TF-COF) complexes in nuclear extracts and quantifies the impact of NCVs on their binding. We demonstrate CASCADE sensitivity in characterizing condition-specific recruitment of COFs p300 and RBBP5 (MLL subunit) to the CXCL10 promoter in lipopolysaccharide (LPS)-stimulated human macrophages and quantify the impact of all possible NCVs. To demonstrate applicability to NCV screens, we profile TF-COF binding to = 1,700 single-nucleotide polymorphism quantitative trait loci (SNP-QTLs) in human macrophages and identify perturbed ETS domain-containing complexes. CASCADE will facilitate high throughput testing of molecular mechanisms of NCVs for diverse biological applications.

引用

页数：21

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