Studies in mouse, human, and chicken suggest that activationinduced deaminase (AID) is involved in three known processes leading to antibody diversification: somatic hypermutation, gene conversion, and class-switch recombination. Developing rabbit appendix provides a particularly good site for studying all three of these B cell maturation events. We report here successful cloning of rabbit AID and isolation of AID protein from rabbit appendix-cell nuclear and cytoplasmic extracts. We succeeded in identifying and locating AID protein in cells by immunohistochemical and immunofluorescent staining techniques and examined colocalization of AID and other molecules important for Ab diversification. This report extends our knowledge about AID to a mammalian species that uses gene conversion to diversify rearranged Ig genes. Although much work remains to understand fully the mechanism of action of AID and its association with other cellular components, the rabbit system now offers a particularly useful model for future studies of these dynamics. mass spectrometry ͉ gene conversion ͉ somatic hypermutation T he rabbit is an excellent animal model for study of somatic hypermutation (SHM) and gene conversion (GC) of rearranged variable regions (V) of Ab heavy (H) and light (L) chain genes. The appendix of neonatal rabbits is a critical site for development of the primary Ab repertoire (1, 2). Rearrangements of H and L chain genes occur in sites including fetal liver, omentum, and bone marrow. After birth, B cells with rearranged genes migrate into gut-associated lymphoid tissue such as the appendix. Gut microflora are required for B cells to proliferate and develop in appendix follicles (3). At Ϸ3 wk of age, diversification of rearranged gene sequences by GC and SHM starts within the appendix-follicle microenvironment (2). GC diversifies sequences encoding V regions of H and L chains through introduction of sequences from upstream donor V gene segments. B cells that have undergone class-switch recombination (CSR), particularly to IgA, are also found in rabbit appendix at Ϸ3 wk of age (2). Activation-induced deaminase (AID) is involved in three processes of Ab diversification and maturation, SHM, CSR (4-7), and GC (8,9), that all coexist in young rabbit appendix. Thus far, the only published evidence for the role of AID in GC comes from two studies showing that in the chicken DT40 bursal tumor cell line that carries out GC in vitro, no GC occurs when AID is knocked out on both chromosomes (8, 9). Although there are several hypotheses about how AID functions, data are accumulating that suggest that AID deaminates cytosine to uracil on the non-template strand of DNA during transcription (10). It is also possible that AID deaminates cytidine to uridine on an unknown mRNA (11,12). Data are still emerging that suggest AID has different roles and cofactor interactions when participating in CSR and SHM (13,14).We used 1-to 6-wk-old ali͞ali V H mutant rabbits to study rabbit AID. These mutants have a small (Ϸ10 kb) deletion encompas...