CTCF-binding elements mediate control of V(D)J recombination

Immunoglobulin heavy chain (IgH) variable region exons are assembled from V H , D and J H gene segments in developing B lymphocytes. Within the 2.7-megabase mouse Igh locus, V(D)J recombination is regulated to ensure specific and diverse antibody repertoires. Here we report in mice a key Igh V(D)J recombination regulatory region, termed intergenic control region 1 (IGCR1), which lies between the V H and D clusters. Functionally, IGCR1 uses CTCF looping/insulator factor-binding elements and, correspondingly, mediates Igh loops containing distant enhancers. IGCR1 promotes normal B-cell development and balances antibody repertoires by inhibiting transcription and rearrangement of D H -proximal V H gene segments and promoting rearrangement of distal V H segments. IGCR1 maintains ordered and lineage-specific V H (D)J H recombination by suppressing V H joining to D segments not joined to J H segments, and V H to DJ H joins in thymocytes, respectively. IGCR1 is also required for feedback regulation and allelic exclusion of proximal V H -to-DJ H recombination. Our studies elucidate a long-sought Igh V(D)J recombination control region and indicate a new role for the generally expressed CTCF protein. Enforcing order in heavy chains The variable region of the immunoglobulin heavy chain (IgH) is generated by selecting one segment each from the V H , D and J H loci. Many studies have proposed the existence of a control region between the V H and D loci that would regulate V H -to-D recombination, but its identity has been elusive. Frederick Alt and colleagues have now located this regulatory sequence, IGCR1 (intergenic control region 1), and show that it uses CTCF sites to promote looping and interaction with distal enhancer elements. It also suppresses other events that would disrupt the ordered rearrangement of the V H , D and J H loci.