Antibody repertoires generated by VH replacement and direct VH to JH joining

The immunoglobulin heavy chain repertoire is generated by somatic rearrangement of variable (V-H), diversity (D-H), and joining (J(H)) elements. It can be further diversified by V-H replacement, where nonrearranged V-H genes invade preexisting V(H)D(H)J(H) joints. To study the impact and mechanism of V-H replacement, we generated mice in which antibody production depends on the replacement of a nonproductive V(H)D(H)J(H) rearrangement inserted into its physiological position in the immunoglobulin heavy chain locus. In these mice a highly diverse heavy chain repertoire resulted from V-H replacement and a second process of noncanonical V(D)J recombination, direct V-H to J(H) joining. V-H replacement rarely generated detectable sequence duplications but often proceeded through recombination between the conserved homologous sequences at the 3' end of V-H. Thus, V-H replacement is an efficient mechanism of antibody diversification, and its impact on the overall antibody repertoire could be greater than anticipated because it frequently leaves no molecular footprint.