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 (V-H), a diversity (D-H), and a joining (J(H)) gene segment. Here, we report that in the absence of intergenic control region 1 (IGCR1), the intronic enhancer (E mu) associates with the next available CTCF binding site located close to V(H)81X via putative heterotypic interactions involving YY1 and CTCF. The alternate E mu/V(H)81X loop leads to formation of a distorted recombination center and altered D-H rearrangements and disrupts chromosome conformation that favors distal V-H recombination. Cumulatively, these features drive highly skewed, Em-dependent recombination of V(H)81X. Sequential deletion of CTCF binding regions on IGCR1-deleted alleles suggests that they influence recombination of single proximal V-H gene segments. Our observations demonstrate that Em interacts differently with IGCR1- or V-H-associated CTCF binding sites and thereby identify distinct roles for insulator-like elements in directing enhancer activity.