Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [ATAC-seq]

Cohesin stalling at CTCF binding sites represents one of the main principles of interphase chromosome organization. In the current studies, we dissect the role of cohesin and CTCF, both alone and in combination, in 3D genome organization by depleting these proteins using acute protein degradation techniques. By systematic examination of interactomic, epigenomic and transcriptomic changes using various sequencing techniques, our studies reveal the functions of cohesin and CTCF in mediating the formation of chromatin loops, topologically associating domains, chromosome compartments and nuclear lamina associating domains. Our studies describe fundamental principles of how the architectural proteins contribute to genome folding at multiple genomic scales and transcriptional regulation. Acute depletion of CTCF WAPL and RAD21 using AID-mediated protein depletion, followed by ATAC-seq as described (Liu et al., 2017).