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

oleh: David Bray, Heather Hook, Rose Zhao, Jessica L. Keenan, Ashley Penvose, Yemi Osayame, Nima Mohaghegh, Xiaoting Chen, Sreeja Parameswaran, Leah C. Kottyan, Matthew T. Weirauch, Trevor Siggers

Format: Article
Diterbitkan: Elsevier 2022-02-01

Deskripsi

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.