Contribution of V(H) Replacement Products in Mouse Antibody Repertoire

V(H) replacement occurs through RAG-mediated recombination between the cryptic recombination signal sequence (cRSS) near the 3′ end of a rearranged V(H) gene and the 23-bp RSS from an upstream unrearranged V(H) gene. Due to the location of the cRSS, V(H) replacement leaves a short stretch of nucleotides from the previously rearranged V(H) gene at the newly formed V-D junction, which can be used as a marker to identify V(H) replacement products. To determine the contribution of V(H) replacement products to mouse antibody repertoire, we developed a Java-based V(H) Replacement Footprint Analyzer (V(H)RFA) program and analyzed 17,179 mouse IgH gene sequences from the NCBI database to identify V(H) replacement products. The overall frequency of V(H) replacement products in these IgH genes is 5.29% based on the identification of pentameric V(H) replacement footprints at their V-D junctions. The identified V(H) replacement products are distributed similarly in IgH genes using most families of V(H) genes, although different families of V(H) genes are used differentially. The frequencies of V(H) replacement products are significantly elevated in IgH genes derived from several strains of autoimmune prone mice and in IgH genes encoding autoantibodies. Moreover, the identified V(H) replacement footprints in IgH genes from autoimmune prone mice or IgH genes encoding autoantibodies preferentially encode positively charged amino acids. These results revealed a significant contribution of V(H) replacement products to the diversification of antibody repertoire and potentially, to the generation of autoantibodies in mice.