Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [ChIP-seq]

During V(D)J recombination RAG proteins introduce DNA double strand breaks (DSBs) adjacent to conserved recombination signal sequences (RSS) that contain either 12- or 23-nucleotide spacer regions. Coordinated cleavage following the “12/23” rule predicts that DSBs at variable (V) gene segments should not exceed the level of breakage at joining (J) segments, thereby ensuring that V regions do not engage in undesirable recombination events with one another. Here we report abundant RAG dependent DSBs at a multitude of V? gene segments within the Ig? locus independent of V-J rearrangement. We discover that a large fraction of V? gene segments are flanked not only by a bone-fide 12 spacer, but also an overlapping, 23 spacer flipped RSS. These compatible pairs of RSS mediate recombination and deletion inside the V? cluster even in the complete absence of J? gene segments, and support a novel recombination center (RC) independent of the conventional J?-centered RC. We propose a model that explains V? gene segment usage by taking into account not only the probability of V-to-J rearrangement but also the surprisingly frequent, evolutionarily conserved intra-V? cluster recombination events. These findings shed light on the diverse molecular strategies that shape the primary antigen receptor repertoires. Overall design: ChIP-seq profile in Abelson-transformed mouse Pre-B cells.