PT  - JOURNAL ARTICLE
AU  - David Bray
AU  - Heather Hook
AU  - Rose Zhao
AU  - Jessica L. Keenan
AU  - Ashley Penvose
AU  - Yemi Osayame
AU  - Nima Mohaghegh
AU  - Trevor Siggers
TI  - Customizable high-throughput platform for profiling cofactor recruitment to DNA to characterize cis-regulatory elements and screen non-coding single-nucleotide polymorphisms
AID  - 10.1101/2020.04.21.053710
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.04.21.053710
4099  - http://biorxiv.org/content/early/2020/04/22/2020.04.21.053710.short
4100  - http://biorxiv.org/content/early/2020/04/22/2020.04.21.053710.full
AB  - Determining how DNA variants affect the binding of regulatory complexes to cis-regulatory elements (CREs) and non-coding single-nucleotide polymorphisms (ncSNPs) is a challenge in genomics. To address this challenge, we have developed CASCADE (Comprehensive ASsessment of Complex Assembly at DNA Elements), which is a protein-binding microarray (PBM)-based approach that allows for the high-throughput profiling of cofactor (COF) recruitment to DNA sequence variants. The method also enables one to infer the identity of the transcription factor-cofactor (TF-COF) complexes involved in COF recruitment. We use CASCADE to characterize regulatory complexes binding to CREs and SNP quantitative trait loci (SNP-QTLs) in resting and stimulated human macrophages. By profiling the recruitment of the acetyltransferase p300 and MLL methyltransferase component RBBP5, we identify key regulators of the chemokine CXCL10, and by profiling a set of five functionally diverse COFs we identify a prevalence of ETS sites mediating COF recruitment at SNP-QTLs in macrophages. Our results demonstrate that CASCADE is a customizable, high-throughput platform to link DNA variants with the biophysical complexes that mediate functions such as chromatin modification or remodeling in a cell state-specific manner.Competing Interest StatementThe authors have declared no competing interest.