Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire

Summary: During V(D)J recombination, RAG proteins introduce DNA double-strand breaks (DSBs) at recombination signal sequences (RSSs) that contain either 12- or 23-nt spacer regions. Coordinated 12/23 cleavage predicts that DSBs at variable (V) gene segments should equal the level of breakage at joining (J) segments. Contrary to this, here we report abundant RAG-dependent DSBs at multiple Vκ gene segments independent of V-J rearrangement. We find that a large fraction of Vκ gene segments are flanked not only by a bone-fide 12 spacer but also an overlapping, 23-spacer flipped RSS. These compatible pairs of RSSs mediate recombination and deletion inside the Vκ cluster even in the complete absence of Jκ gene segments and support a V(D)J recombination center (RC) independent of the conventional Jκ-centered RC. We propose an improved model of Vκ-Jκ repertoire formation by incorporating these surprisingly frequent, evolutionarily conserved intra-Vκ cluster recombination events. : Shinoda et al. demonstrate previously unknown, frequent RAG-dependent recombination within the Ig Vκ gene cluster, which is mediated by evolutionarily conserved flipped RSS embedded in bona fide RSS. These intra-Vκ cluster recombination events alter the available Vκ gene pool by deleting Vκ segments and shape the Vκ-Jκ immune repertoire. Keywords: END-seq, HTGTS, ig kappa locus, ig repertoire, immunoglobulin, RAG, recombination center, recombination signal sequence, variable, VDJ recombination