The DNA-Binding Protein CTCF Limits Proximal V kappa Recombination and Restricts kappa Enhancer Interactions to the Immunoglobulin kappa Light Chain Locus

Regulation of immunoglobulin (Ig) V(D)J gene rear-rangement is dependent on higher-order chromatin organization. Here, we studied the in vivo function of the DNA-binding zinc-finger protein CTCF, which regulates interactions between enhancers and promoters. By conditional deletion of the Ctcf gene in the B cell lineage, we demonstrate that loss of CTCF allowed Ig heavy chain recombination, but pre-B cell proliferation and differentiation was severely impaired. In the absence of CTCF, the Ig kappa light chain locus showed increased proximal and reduced distal V kappa usage. This was associated with enhanced proximal V kappa and reduced J kappa germline transcription. Chromosome conformation capture experiments demonstrated that CTCF limits interactions of the Ig kappa enhancers with the proximal V(kappa) gene region and prevents inappropriate interactions between these strong enhancers and elements outside the Ig kappa locus. Thus, although Ig gene recombination can occur in the absence of CTCF, it is a critical factor determining V kappa segment choice for recombination.