Promoter- and enhancer-dependent cohesin loading initiates chromosome looping to fold Tcrb loci for long-range recombination

Cohesin-mediated chromosome looping regulates diverse processes, including antigen receptor (AgR) gene assembly by V(D)J recombination. To understand the mechanisms that coordinate genome topologies, we focused on a genetically tractable AgR locus, Tcrb. Cohesin loading and initiation of loop extrusion (LE) from a nearby CTCF-binding element (CBE) required the promoter of the most 5'Vb segment, creating long-range contacts with downstream DJb segments in the recombination center (RC). CBEs flanking the RC have multiple functions: termination of LE originating in the Vb cluster, initiation of LE in the RC, and insulation of enhancer activity. Deletion of the Tcrb super-enhancer abolished LE from the neighboring RC but spared long-range contacts, indicating that unidirectional LE from upstream Vb segments was sufficient. Thus, Vb promoter- or enhancer-dependent cohesin loading initiates LE in opposite directions across the locus to assemble a broad Tcrb repertoire, a finding that has broad implications for genomic architecture and function.