Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus

Immunoglobulin heavy-chain (IgH) genes are assembled by DNA rearrangements that juxtapose a variable (VH), a diversity (DH), and a joining (JH) gene segment. Here, we report that in the absence of intergenic control region 1 (IGCR1), the intronic enhancer (Eμ) associates with the next available CTCF binding site located close to VH81X via putative heterotypic interactions involving YY1 and CTCF. The alternate Eμ/VH81X loop leads to formation of a distorted recombination center and altered DH rearrangements and disrupts chromosome conformation that favors distal VH recombination. Cumulatively, these features drive highly skewed, Eμ-dependent recombination of VH81X. Sequential deletion of CTCF binding regions on IGCR1-deleted alleles suggests that they influence recombination of single proximal VH gene segments. Our observations demonstrate that Eμ interacts differently with IGCR1- or VH-associated CTCF binding sites and thereby identify distinct roles for insulator-like elements in directing enhancer activity. [Display omitted] •Eμ loops to next CTCF-binding elements close to VH81X in the absence of IGCR1•Newly formed loop leads to an altered recombination center and reduced DFL16.1 usage•Loss of Eμ/IGCR1 interaction disrupts chromatin conformation of distal VH genes•Sequential deletion of CTCF binding regions leads to sequential proximal VH utilization Qiu et al. highlight mechanisms by which enhancer sequestration by different CTCF sites shapes chromatin structure to regulate DNA rearrangement at the IgH locus. Their observations identify distinct roles for insulator-like elements in modulating enhancer function.