Journal Article

Loop extrusion mediates physiological Igh locus contraction for RAG scanning

Zhang, Xuefei, Zhao, Lijuan, Chapdelaine-Williams, Aimee M., Kyritsis, Nia, Zhang, Yiwen, Hu, Hongli, Johnson, Kerstin, Ba, Zhaoqing, Lou, Jiangman, Lee, Cheng-Sheng, Casellas, Rafael, Chen, Huan, Ye, Adam Yongxin, Yoon, Hye Suk, Lin, Sherry, Dai, Hai-Qiang, Conte, Andrea, Alt, Frederick W.

2021

Overview

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. Long-distance V(D)J recombination is facilitated by contraction of the Igh locus and linear RAG scanning along chromatin, both driven by cohesin-mediated loop extrusion, which allows recombination of widely separated gene segments to occur.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 13/1 / 13/100 / 13/106 / 13/109 / 13/31 / 38/35 / 631/250/1619/40/1774 / 631/337/149 / 64/60 / Animals / B cells / B-Lymphocytes - cytology / B-Lymphocytes - enzymology / B-Lymphocytes - metabolism / Binding / Cell Line / Cell lines / Cells, Cultured / Chromatin / Cohesin / Contraction / Convergence / Depletion / Deregulation / DNA-Binding Proteins - deficiency / DNA-Binding Proteins - genetics / DNA-Binding Proteins - metabolism / Down-Regulation / Endonuclease / Endonucleases - deficiency / Endonucleases - genetics / Endonucleases - metabolism / Enzymes / Extrusion / G1 Phase Cell Cycle Checkpoints / Genetic aspects / Genomes / Heavy chains / High-Throughput Nucleotide Sequencing / Homeodomain Proteins - genetics / Homeodomain Proteins - metabolism / Homology / Humanities and Social Sciences / Immunoglobulin Heavy Chains - genetics / Immunoglobulins / Loci / Lymphocytes B / Mice / Mice, Inbred C57BL / multidisciplinary / Nucleic Acid Conformation / Physiological aspects / Proteins - genetics / Proteins - metabolism / Scanning / Science / Science (multidisciplinary) / Telomeres / Unloading / Upstream / V(D)J recombination / V(D)J Recombination - genetics