CTCF-mediated chromatin topology enables receptor editing to enforce a central B-cell tolerance checkpoint [RNA-seq_IGK repertoire]

The generation of a diverse yet self-tolerant B cell repertoire is fundamental to adaptive immunity and is achieved through the ordered process of V(D)J recombination. In mice, Igκ represents the dominant light chain, while Igλ rearrangement serves as a secondary response to nonproductive or autoreactive Igκ recombination — a process known as receptor editing. Recombination at the RS element deletes the Igκ constant exon, silencing the locus and enabling Igλ expression. Yet the epigenetic regulatory framework that orchestrates this critical tolerance checkpoint in immature B cells remains unresolved. Here, we identify a CTCF-binding element (CBE) embedded within the 3′-Igκ super-enhancer (3′-SEκ) that governs receptor editing and directs the κ-to-λ switch essential for Igλ⁺ B cell development in vivo. Mechanistically, deletion of this insulator element abrogates chromatin looping essential for receptor editing and concomitantly activates a latent enhancer program within the 3′-SEκ, driving aberrant Vκ recombination and rewiring Igκ chromatin architecture through disrupted CTCF boundary function. Notably, loss of this CBE swiftly leads to elevated autoantibody production, demonstrating that CBE-mediated chromatin architecture shapes B cell fate by constraining autoreactivity. Collectively, these findings establish CTCF-dependent chromatin topology as a checkpoint that couples three-dimensional genome organization with antigen-driven receptor editing, to establish self-tolerance.