Loop extrusion mediates physiological Igh locus contraction for RAG scanning

RAG endonuclease initiates Igh V(D)J recombination in progenitor B cells by binding a J H -recombination signal sequence (RSS) within a recombination centre (RC) and then linearly scanning upstream chromatin, presented by loop extrusion mediated by cohesin, for convergent D-RSSs 1 , 2 . The utilization of convergently oriented RSSs and cryptic RSSs is intrinsic to long-range RAG scanning 3 . Scanning of RAG from the DJ H -RC-RSS to upstream convergent V H -RSSs is impeded by D-proximal CTCF-binding elements (CBEs) 2 – 5 . Primary progenitor B cells undergo a mechanistically undefined contraction of the V H locus that is proposed to provide distal V H s access to the DJ H -RC 6 – 9 . Here we report that an inversion of the entire 2.4-Mb V H locus in mouse primary progenitor B cells abrogates rearrangement of both V H -RSSs and normally convergent cryptic RSSs, even though locus contraction still occurs. In addition, this inversion activated both the utilization of cryptic V H -RSSs that are normally in opposite orientation and RAG scanning beyond the V H locus through several convergent CBE domains to the telomere. Together, these findings imply that broad deregulation of CBE impediments in primary progenitor B cells promotes RAG scanning of the V H locus mediated by loop extrusion. We further found that the expression of wings apart-like protein homologue (WAPL) 10 , a cohesin-unloading factor, was low in primary progenitor B cells compared with v-Abl -transformed progenitor B cell lines that lacked contraction and RAG scanning of the V H locus. Correspondingly, depletion of WAPL in v-Abl -transformed lines activated both processes, further implicating loop extrusion in the locus contraction mechanism.