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

• Main Authors: David Bray (Author), Heather Hook (Author), Rose Zhao (Author), Jessica L. Keenan (Author), Ashley Penvose (Author), Yemi Osayame (Author), Nima Mohaghegh (Author), Xiaoting Chen (Author), Sreeja Parameswaran (Author), Leah C. Kottyan (Author), Matthew T. Weirauch (Author), Trevor Siggers (Author)
• Format: Book
• Published: Elsevier, 2022-02-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.
• Notes: 2666-979X; 10.1016/j.xgen.2022.100098
• Keywords: cofactor; transcription factor; recruitment; single-nucleotide polymorphism; screen; logo; Genetics; QH426-470; Internal medicine; RC31-1245
• Source: Cell Genomics, Vol 2, Iss 2, Pp 100098- (2022)

Summary: 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.