PMID- 33442057 OWN - NLM STAT- MEDLINE DCOM- 20210309 LR - 20230127 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 590 IP - 7845 DP - 2021 Feb TI - Loop extrusion mediates physiological Igh locus contraction for RAG scanning. PG - 338-343 LID - 10.1038/s41586-020-03121-7 [doi] AB - 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. FAU - Dai, Hai-Qiang AU - Dai HQ AUID- ORCID: 0000-0003-4337-9770 AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. hai-qiang.dai@childrens.harvard.edu. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. hai-qiang.dai@childrens.harvard.edu. FAU - Hu, Hongli AU - Hu H AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Lou, Jiangman AU - Lou J AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Ye, Adam Yongxin AU - Ye AY AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Ba, Zhaoqing AU - Ba Z AUID- ORCID: 0000-0002-8431-5469 AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Zhang, Xuefei AU - Zhang X AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Zhang, Yiwen AU - Zhang Y AUID- ORCID: 0000-0003-4883-0743 AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Zhao, Lijuan AU - Zhao L AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Yoon, Hye Suk AU - Yoon HS AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Chapdelaine-Williams, Aimee M AU - Chapdelaine-Williams AM AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Kyritsis, Nia AU - Kyritsis N AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Chen, Huan AU - Chen H AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Johnson, Kerstin AU - Johnson K AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Lin, Sherry AU - Lin S AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Conte, Andrea AU - Conte A AD - Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA. AD - Center of Cancer Research, NCI, NIH, Bethesda, MD, USA. FAU - Casellas, Rafael AU - Casellas R AD - Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA. AD - Center of Cancer Research, NCI, NIH, Bethesda, MD, USA. FAU - Lee, Cheng-Sheng AU - Lee CS AUID- ORCID: 0000-0002-0765-2410 AD - Department of Life Science, National Tsing Hua University, Institute of Molecular and Cellular Biology, Hsinchu, Taiwan, R.O.C.. cslee@life.nthu.edu.tw. FAU - Alt, Frederick W AU - Alt FW AUID- ORCID: 0000-0002-0583-1271 AD - Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. alt@enders.tch.harvard.edu. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. alt@enders.tch.harvard.edu. LA - eng GR - R01 AI020047/AI/NIAID NIH HHS/United States GR - R37 AI020047/AI/NIAID NIH HHS/United States GR - T32 AI007386/AI/NIAID NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20210113 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA-Binding Proteins) RN - 0 (Homeodomain Proteins) RN - 0 (Immunoglobulin Heavy Chains) RN - 0 (Proteins) RN - 0 (Rag2 protein, mouse) RN - 0 (WAPL protein, mouse) RN - 128559-51-3 (RAG-1 protein) RN - EC 3.1.- (Endonucleases) SB - IM MH - Animals MH - B-Lymphocytes/cytology/enzymology/*metabolism MH - Cell Line MH - Cells, Cultured MH - DNA-Binding Proteins/deficiency/genetics/*metabolism MH - Down-Regulation MH - Endonucleases/deficiency/genetics/*metabolism MH - G1 Phase Cell Cycle Checkpoints MH - High-Throughput Nucleotide Sequencing MH - Homeodomain Proteins/genetics/*metabolism MH - Immunoglobulin Heavy Chains/*genetics MH - Mice MH - Mice, Inbred C57BL MH - *Nucleic Acid Conformation MH - Proteins/genetics/metabolism MH - V(D)J Recombination/genetics PMC - PMC9037962 MID - NIHMS1650045 COIS- The authors declare no competing financial interests. F.W.A. is a co-founder of Otoro Biopharmaceuticals. EDAT- 2021/01/15 06:00 MHDA- 2021/03/10 06:00 PMCR- 2022/04/25 CRDT- 2021/01/14 05:45 PHST- 2020/06/05 00:00 [received] PHST- 2020/11/25 00:00 [accepted] PHST- 2021/01/15 06:00 [pubmed] PHST- 2021/03/10 06:00 [medline] PHST- 2021/01/14 05:45 [entrez] PHST- 2022/04/25 00:00 [pmc-release] AID - 10.1038/s41586-020-03121-7 [pii] AID - 10.1038/s41586-020-03121-7 [doi] PST - ppublish SO - Nature. 2021 Feb;590(7845):338-343. doi: 10.1038/s41586-020-03121-7. Epub 2021 Jan 13.