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 VH 81X via putative heterotypic interactions involving YY1 and CTCF. The alternate Eμ/VH 81X 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 VH 81X. 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.