Fundamental roles of chromatin loop extrusion in antibody class switching

Antibody class switch recombination (CSR) in B lymphocytes replaces immunoglobulin heavy chain locus (Igh) C mu 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 S mu 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 S mu-upstream DSB-end to an acceptor S-region-downstream DSB-end for deletional CSR12. 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 S mu 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 S mu for deletional CSR. During constitutive S alpha 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 S mu 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.