Fundamental roles of chromatin loop extrusion in antibody class switching

• Published in: Nature (London) 2019-11, Vol.575 (7782), p.385-389
• Main Authors: Zhang, Xuefei, Zhang, Yu, Ba, Zhaoqing, Kyritsis, Nia, Casellas, Rafael, Alt, Frederick W.
• Format: Article
• Language: English
• Subjects: 13; 13/1; 13/106; 13/31; 13/44; 38; 38/23; 38/90; 38/91; 42/41; 45; 631/208; 631/250/2152/2498; Analysis; Animals; Antibodies; B-cell lymphoma; Cells, Cultured; Chromatin; Chromatin - genetics; Chromosome Pairing; Class switching; Cohesin; Constant region; Cytidine deaminase; Cytidine Deaminase - deficiency; Cytidine Deaminase - metabolism; Cytokines; Deamination; Deoxyribonucleic acid; DNA; DNA repair; Enhancers; Exons; Extrusion; Genetic aspects; Genetic recombination; Genomes; Heavy chains; Humanities and Social Sciences; Identification and classification; Immunoglobulin Class Switching; Immunoglobulin Heavy Chains; Immunoglobulins; Influence; Insertion; Lesions; Lymphocytes; Lymphocytes B; Lymphoma; Mice, Knockout; multidisciplinary; Mutation; Recombination; Science; Science (multidisciplinary); Sequence Deletion; Structure; Switch genes; Transcription; Transcription, Genetic; Viral antibodies
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-019-1723-0

Antibody class switch recombination (CSR) in B lymphocytes replaces immunoglobulin heavy chain locus ( Igh ) Cμ constant region exons (C H s) with one of six C H s lying 100–200 kb downstream 1 . Each C H is flanked upstream by an I promoter and long repetitive switch (S) region 1 . Cytokines and activators induce activation-induced cytidine deaminase (AID) 2 and I-promoter transcription, with 3′ IgH regulatory region (3′ IgHRR) enhancers controlling the latter via I-promoter competition for long-range 3′ IgHRR interactions 3 – 8 . Transcription through donor Sμ and an activated downstream acceptor S-region targets AID-generated deamination lesions at, potentially, any of hundreds of individual S-region deamination motifs 9 – 11 . General DNA repair pathways convert these lesions to double-stranded breaks (DSBs) and join an Sμ-upstream DSB-end to an acceptor S-region-downstream DSB-end for deletional CSR 12 . AID-initiated DSBs at targets spread across activated S regions routinely participate in such deletional CSR joining 11 . Here we report that chromatin loop extrusion underlies the mechanism 11 by which IgH organization in cis promotes deletional CSR. In naive B cells, loop extrusion dynamically juxtaposes 3′ IgHRR enhancers with the 200-kb upstream Sμ to generate a CSR centre (CSRC). In CSR-activated primary B cells, I-promoter transcription activates cohesin loading, leading to generation of dynamic subdomains that directionally align a downstream S region with Sμ for deletional CSR. During constitutive Sα CSR in CH12F3 B lymphoma cells, inversional CSR can be activated by insertion of a CTCF-binding element (CBE)-based impediment in the extrusion path. CBE insertion also inactivates upstream S-region CSR and converts adjacent downstream sequences into an ectopic S region by inhibiting and promoting their dynamic alignment with Sμ in the CSRC, respectively. Our findings suggest that, in a CSRC, dynamically impeded cohesin-mediated loop extrusion juxtaposes proper ends of AID-initiated donor and acceptor S-region DSBs for deletional CSR. Such a mechanism might also contribute to pathogenic DSB joining genome-wide. Chromatin loop extrusion has fundamental mechanistic roles in immunoglobulin heavy chain class switch recombination.