Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2 [ChIP-seq]

Cohesin-mediated loop extrusion is central to IgH V(D)J recombination in early developing B cells, driving D-to-JH rearrangements and VH-to-DJH rearrangements, with the latter step regulated by the cohesin release factor WAPL. Here, we investigate the distinct contributions of two cohesin subunits, STAG1 and STAG2, which are incorporated in the somatic cohesin variants, cohesin-STAG1 and cohesin-STAG2, respectively. Using WAPL-sufficient mouse v-Abl pro-B cells to model the D-to-JH recombination stage, we show that STAG2 promotes balanced D-to-JH joining and restrains STAG1 expression. Loss of STAG2 elevates cohesin-STAG1 occupancy on chromatin, leading to premature long-range loop formation and expanded VH usage at the expense of distal DH usage. This phenotype persists in the absence of the cohesin acetyltransferase ESCO1 but requires the N-terminal YDF motif of CTCF, which protects cohesin from WAPL-mediated chromatin release. In WAPL-depleted cells modeling the VH-to-DJH recombination stage, the CTCF N-terminus is dispensable and both cohesin variants act cooperatively to establish a diverse VH repertoire. Thus, our findings uncover context-dependent and complementary roles of these two cohesin variants in shaping antibody gene diversity, and also highlight a regulatory axis between STAG1, STAG2, and CTCF in controlling long-range chromatin dynamics.