Somatic hypermutation (SHM) of the Ig genes is required for affinity maturation of the humoral response to foreign antigens. Activation-induced cytidine deaminase (AID), which is specifically expressed in germinal center centroblasts, is indispensable for this process. Expression of AID is sufficient to activate SHM in hybridomas, non-B cells, and Escherichia coli, suggesting that it initiates the mutational process by deaminating DNA. However, the cisacting sequences that are responsible for targeting AID activity to the variable (V) region of Ig genes are unknown. Here we show that expression of AID in B cell lines (i.e., Burkitt's lymphoma Ramos and hybridoma P1-5) not only causes hypermutation of Ig sequences, but also of the AID transgene itself. Because it is possible that B cell-specific transacting factors bind to and recruit the ''mutator'' to the AID transgene, we tested whether the AID transgene can mutate in non-B cells. Indeed, we show that expression of AID in Chinese hamster ovary cells causes SHM of both the Ig and AID transgenes. These data suggest that high transcription rates alone may predispose any gene to mutation by AID but do not preclude that there are specific B cell factors that account for the extremely high rate of V mutation in vivo and its targeting to the V region.A ffinity maturation of the antibody response is mediated by somatic hypermutation (SHM) of the antibody genes with subsequent selection of B cell clones that produce higher affinity antibodies to the immunizing antigen. SHM causes point mutations and occasional deletions and insertions at very high rates of Ϸ10 Ϫ3 bp per generation and occurs during the centroblast stage of B cell differentiation. The mutations are restricted to the variable region (V region) that encodes the antibody binding site and to sequences that are Ϸ1.5 kb downstream from the Ig promoter. Some of these mutations increase the affinity of the antibody so that it can neutralize viruses and toxins and inactivate pathogenic organisms.Mice and humans with mutations in activation-induced cytidine deaminase (AID) have defects in SHM (1, 2), class-switch recombination (1), and gene conversion (3, 4). Based on the sequence similarity of AID to the RNA-editing enzyme APOBEC-1 (5), it was postulated that AID might function by editing a specific message that results in the production of an altered protein that subsequently causes mutation (6). However, the higher than expected number of transition mutations in V regions (7) raises the possibility that AID might be a DNAspecific cytidine deaminase that converts C to U nucleotides directly in the DNA of the V region. In fact, we recently showed that AID induced the P1-5 hybridoma to exclusively mutate G⅐C bp, and most of these mutations were transition mutations (8). With the finding that AID can induce SHM in non-B cells (9) and Escherichia coli (4), it is more likely that AID is a DNA-specific cytidine deaminase.The mechanism for targeting of SHM to the V region of Ig genes is not known. Interestingly, SHM h...