Physiological role of the 3′IgH CBEs super-anchor in antibody class switching

IgH class switch recombination (CSR) replaces Cμ constant region (C(H)) exons with one of six downstream C(H)s by joining transcription-targeted double-strand breaks (DSBs) in the Cμ switch (S) region to DSBs in a downstream S region. Chromatin loop extrusion underlies fundamental CSR mechanisms including 3′IgH regulatory region (3′IgHRR)-mediated S region transcription, CSR center formation, and deletional CSR joining. There are 10 consecutive CTCF-binding elements (CBEs) downstream of the 3′IgHRR, termed the “3′IgH CBEs.” Prior studies showed that deletion of eight 3′IgH CBEs did not detectably affect CSR. Here, we report that deletion of all 3′IgH CBEs impacts, to varying degrees, germline transcription and CSR of upstream S regions, except that of Sγ1. Moreover, deletion of all 3′IgH CBEs rendered the 6-kb region just downstream highly transcribed and caused sequences within to be aligned with Sμ, broken, and joined to form aberrant CSR rearrangements. These findings implicate the 3′IgH CBEs as critical insulators for focusing loop extrusion-mediated 3′IgHRR transcriptional and CSR activities on upstream C(H) locus targets.