CTCF and cohesin cooperatively mediate the cell-type specific interchromatin interaction between Bcl11b and Arhgap6 loci.

CCCTC-binding factor (CTCF) is a master organizer of genome spatial organization and plays an important role in mediating extensive chromatin interactions. Circular chromosome conformation capture (4C) is a high-throughput approach that allows genome-wide screening for unknown potential interaction partners. Using a conserved CTCF binding site on the Bcl11b locus as bait, an interaction partner at the Arhgap6 locus on a different chromosome was identified by 4C. Additional experiments verified that the interchromatin interaction between the Bcl11b and Arhgap6 loci was cell-type specific, which was cooperatively mediated by CTCF and cohesin. Functional analysis showed that the interchromatin interaction partners were repressing regulatory elements. These results indicate that interaction chromatin loops regulate the expression of the relevant genes.