CTCF and cohesin regulate chromatin loop stability with distinct dynamics

The study investigates the nuclear organization and the binding dynamics of CTCF and cohesin by super-resolution microscopy and ChIP-seq. We determined the genome-wide binding profile of CTCF and Rad21 cohesin subunit in wild type mouse ES cells and compared them to a double FLAG-Halo-mCTCF/mRad21-SNAPf-V5 knock-in mES line, generated by CRISPR/Cas9-mediated genome editing to perform imaging experiments. Overall design: ChIP-Seq of CTCF and Rad21 cohesin subunit in wild type mouse ES cells (WT) and in mouse ES cells homozygous for FLAG-Halo-CTCF and Rad21-SNAPf-V5 (C59 clone). ChIP-Seq libraries were prepared independently from two ChIP biological replicates, using normal serum IgGs as a control, and including total inputs as reference datasets.