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

Cohesin-mediated loop extrusion is central to IgH V(D)J recombination in early developing B cells, driving D-to-J_H rearrangements and V_H-to-DJ_H 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-J_H recombination stage, we show that STAG2 promotes balanced D-to-J_H joining and restrains STAG1 expression. Loss of STAG2 elevates cohesin-STAG1 occupancy on chromatin, leading to premature long-range loop formation and expanded V_H usage at the expense of distal D_H 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 V_H-to-DJ_H recombination stage, the CTCF N-terminus is dispensable and both cohesin variants act cooperatively to establish a diverse V_H 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.