Unraveling the cohesin-chromatin interface: identifying protein interactions that modulate chromosome structure and function [ChIP-Seq]

Cohesin is a plieotropic regulator of genom structure and function with several known interactors that aid in regulation of genome organization. A comprehensive cohesin interactome has yet to be established, and we identify several chromatin regulating complexes that interact with the cohesin complex, including the SWI/SNF chromatin remodeling complex. SWI/SNF and cohesin co-localize to enhancers, promoters, and CTCF binding sites as deteremined by overlapping ChIP-seq data from mESCs for the cohesin subunit RAD21 and the SWI/SNF subunit BRG1, CTCF, H3K27ac, and H3K4me3. To assessthe functional implications of the cohesin-SWI/SNF interaction we treated mESCs with one of three small molecule drugs targeting the BRG1 subunit of SWI/SNF (ACBI1, PFI-3, BRM014) for either degradation of the complex or perturbation of SWI/SNF function, then performed ChIP-seq for the RAD21 subunit of cohesin. Differential RAD21 peaks in cells treated with a small molecule compared to DMSO control were assessed for overlap with DNA loops (Micro-C). Overall design: ChIP-seq was performed in wildtype mESCs with five replicates for RAD21 and CTCF. ChIP-seq was performed in mESCs treated with BRG1 targeting drugs (ACBI1 PROTAC, PFI-3 bromodomain inhibitor, or BRM014 ATPase inhibitor) or DMSO as a control in duplicate for RAD21.