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

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

doi:10.1016/j.xgen.2022.100098

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

Cell Genom. 2022 Feb 9;2(2):100098. doi: 10.1016/j.xgen.2022.100098.

Authors

David Bray^{1

2

3

4}, Heather Hook^{1

2

4}, Rose Zhao^{1

2}, Jessica L Keenan^{1

2

3}, Ashley Penvose^{1

2}, Yemi Osayame^{1

2}, Nima Mohaghegh^{1

2}, Xiaoting Chen⁵, Sreeja Parameswaran⁵, Leah C Kottyan^{5

6

7}, Matthew T Weirauch^{5

8

9

6}, Trevor Siggers^{1

2

10

11}

Affiliations

¹ Department of Biology, Boston University, Boston, MA, USA.
² Biological Design Center, Boston University, Boston, MA, USA.
³ Bioinformatics Program, Boston University, Boston, MA, USA.
⁴ These authors contributed equally.
⁵ Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
⁶ Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
⁷ Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.
⁸ Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
⁹ Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
¹⁰ Senior author.
¹¹ Lead contact.

Abstract

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.

Abstract

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