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
Affiliations
David Bray
Department of Biology, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA
Heather Hook
Department of Biology, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
Rose Zhao
Department of Biology, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
Jessica L. Keenan
Department of Biology, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA
Ashley Penvose
Department of Biology, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
Yemi Osayame
Department of Biology, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
Nima Mohaghegh
Department of Biology, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
Xiaoting Chen
Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
Sreeja Parameswaran
Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
Leah C. Kottyan
Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
Matthew T. Weirauch
Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA; Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA; Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
Trevor Siggers
Department of Biology, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA; Corresponding author
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.
