TY - JOUR
T1 - Loop extrusion mediates physiological Igh locus contraction for RAG scanning
AU - Dai, Hai Qiang
AU - Hu, Hongli
AU - Lou, Jiangman
AU - Ye, Adam Yongxin
AU - Ba, Zhaoqing
AU - Zhang, Xuefei
AU - Zhang, Yiwen
AU - Zhao, Lijuan
AU - Yoon, Hye Suk
AU - Chapdelaine-Williams, Aimee M.
AU - Kyritsis, Nia
AU - Chen, Huan
AU - Johnson, Kerstin
AU - Lin, Sherry
AU - Conte, Andrea
AU - Casellas, Rafael
AU - Lee, Cheng Sheng
AU - Alt, Frederick W.
N1 - Funding Information:
Acknowledgements We thank Alt laboratory members for contributions to the study, particularly H.-L. Cheng for advice and help with the embryonic stem cell culture, M. Tian for the EF1 embryonic stem cell line, Y. Zhang for the RAG-expressing retrovirus plasmids, S. Jain for help with cell culture and data analysis, R. Judson and N. Manfredonia for help with the blastocyst injection, and J. Hu for data uploading; as well as E. Bekman at the University of Lisbon for advice on the construction of the degron system, particularly on the inducible expression of OsTIR1. This work was supported by NIH R01 AI020047 (to F.W.A.). H.-Q.D. is a fellow of the Cancer Research Institute (CRI) of New York. H.C. was an NRSA Fellow (T32 AI07386) and was supported by the Leukemia and Lymphoma Society. Z.B. was supported by a CRI fellowship. R.C. is partially funded by the NIH Regulome Project. C.-S.L. was previously supported by a CRI fellowship and is now funded by the Ministry of Science and Technology in Taiwan (MOST109-2636-B-007-004). F.W.A. is an investigator of the Howard Hughes Medical Institute.
Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature Limited.
PY - 2021/2/11
Y1 - 2021/2/11
N2 - RAG endonuclease initiates Igh V(D)J recombination in progenitor B cells by binding a JH-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-RSSs1,2. The utilization of convergently oriented RSSs and cryptic RSSs is intrinsic to long-range RAG scanning3. Scanning of RAG from the DJH-RC-RSS to upstream convergent VH-RSSs is impeded by D-proximal CTCF-binding elements (CBEs)2–5. Primary progenitor B cells undergo a mechanistically undefined contraction of the VH locus that is proposed to provide distal VHs access to the DJH-RC6–9. Here we report that an inversion of the entire 2.4-Mb VH locus in mouse primary progenitor B cells abrogates rearrangement of both VH-RSSs and normally convergent cryptic RSSs, even though locus contraction still occurs. In addition, this inversion activated both the utilization of cryptic VH-RSSs that are normally in opposite orientation and RAG scanning beyond the VH 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 VH 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 VH locus. Correspondingly, depletion of WAPL in v-Abl-transformed lines activated both processes, further implicating loop extrusion in the locus contraction mechanism.
AB - RAG endonuclease initiates Igh V(D)J recombination in progenitor B cells by binding a JH-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-RSSs1,2. The utilization of convergently oriented RSSs and cryptic RSSs is intrinsic to long-range RAG scanning3. Scanning of RAG from the DJH-RC-RSS to upstream convergent VH-RSSs is impeded by D-proximal CTCF-binding elements (CBEs)2–5. Primary progenitor B cells undergo a mechanistically undefined contraction of the VH locus that is proposed to provide distal VHs access to the DJH-RC6–9. Here we report that an inversion of the entire 2.4-Mb VH locus in mouse primary progenitor B cells abrogates rearrangement of both VH-RSSs and normally convergent cryptic RSSs, even though locus contraction still occurs. In addition, this inversion activated both the utilization of cryptic VH-RSSs that are normally in opposite orientation and RAG scanning beyond the VH 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 VH 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 VH locus. Correspondingly, depletion of WAPL in v-Abl-transformed lines activated both processes, further implicating loop extrusion in the locus contraction mechanism.
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U2 - 10.1038/s41586-020-03121-7
DO - 10.1038/s41586-020-03121-7
M3 - Article
C2 - 33442057
AN - SCOPUS:85100057839
SN - 0028-0836
VL - 590
SP - 338
EP - 343
JO - Nature
JF - Nature
IS - 7845
ER -