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

IgH class switch recombination (CSR) replaces C constant region (CH) exons with one of six downstream CHS by joining transcription-targeted DSBs in the C switch (S) region to DSBs in a downstream S region. Chromatin loop extrusion underlies fundamental CSR mechanisms including 3IgH regulatory region (3IgHRR)-mediated S region transcription, CSR center formation, and deletional CSR joining. There are ten consecutive CTCF binding elements (CBEs) downstream of the 3IgHRR, termed the "3IgH CBEs". Prior studies showed that deletion of eight 3IgH CBEs did not detectably affect CSR. Here, we report that deletion of all 3IgH CBEs impacts, to varying degrees, germline transcription and CSR of upstream S regions, except S{gamma}1. Moreover, deletion of all 3IgH CBEs rendered the 6kb region just downstream highly transcribed and caused sequences within to be aligned with S, broken, and joined to form aberrant CSR rearrangements. These findings implicate the 3IgH CBEs as a critical insulator for focusing loop extrusion-mediated 3IgHRR transcriptional and CSR activities on upstream CH locus targets. SignificanceB lymphocytes change antibody heavy chain (IgH) isotypes by a recombination/deletion process called IgH class switch recombination (CSR). CSR involves introduction of DNA breaks into a donor switch (S) region and also into one of six downstream S regions, with joining of the breaks changing antibody isotype. A chromatin super-anchor, of unknown function, is located just downstream of the IgH locus. We show that complete deletion of this super-anchor variably decreases CSR to most S regions and creates an ectopic S region downstream of IgH locus that undergoes aberrant CSR-driven chromosomal rearrangements. Based on these and other findings, we conclude that the super-anchor downstream of IgH is a critical insulator for focusing potentially dangerous CSR rearrangements to the IgH locus.