ChIP-seq data in mESCs show ZFP661 suppresses cohesin binding at CTCF barriers

In this assay, we aimed to investigate the occupancy of ZFP661 in the mouse genome and its possible role in regulating the occupancies of CTCF and cohesin, which are two key factors in establishing 3D chromatin structures. To achieve this, we performed ChIP-seq in ZFP661-3HA endogenously tagged mESCs (for ZFP661), Zfp661 knockout (KO) mESCs (for CTCF and RAD21), and ZFP661-3HA overexpressing (OE) mESCs (for ZFP661, CTCF, RAD21, KAP1, and H3K9me3). Our results reveal that 1) ZFP661 binding peaks were co-occupied with those of CTCF; 2) ZFP661 binds exclusively inside the CTCF loop anchors; and 3) ZFP661 can suppress cohesin binding at CTCF barriers without altering CTCF binding. Overall design: We compared the binding of CTCF and RAD21 on CTCF barriers co-occupied with ZFP661 between wild-type (WT) and Zfp661 KO, as well as between empty vector (EV) control and ZFP661-3HA OE. Each type included two biological replicates.