Figure 1. (a) The schematic shows the murine immunoglobulin (Ig) heavy chain locus before (top) and after (bottom) somatic hypermutation (SHM) and class switch recombination (CSR). Locations of mRNA transcripts encoding the entire heavy chain (V, variable and C, constant exons), and noncoding switch (S)-region transcripts that are required for switch recombination, are shown as arrows beneath the top locus. SHM introduces point mutations (asterisks) into the VDJ-rearranged exon that encodes the Ig V region – the region of the encoded antibody that defines the antigen specificity. CSR is a region-specific recombination event in which a deletion between two S regions occurs. The deletion results in the fusion of a new Ig C-region isotype to the V region. (b) A model for the mechanism of SHM. Activation-induced cytosine deaminase (AID) phosphorylation by PKA prompts interaction with the single-stranded binding protein RPA. AID complexed with RPA deaminates cytosine bases in double-stranded DNA (dsDNA), with a preference for cytosines in the hotpsot sequence AGC/GCT (corresponding to the WRC/GYW motif). Cytosine deamination creates a U–G mispair. Left unrepaired, replication (1) would cause a C/G to T/A mutation. Alternatively, removal of the U by Ung leaves an abasic site (dash) that is uninformative for DNA synthesis by a replication polymerase or translesion polymerase, thereby creating mutations to any possible base at the position of the original deaminated cytosine, and potentially neighbouring bases by a translesion polymerase (2). If the abasic site is processed to a nick (by enzymes such as AP endonuclease, AP endo), and then to a single base pair gap, translesion polymerases could fill-in the single base pair gap or extend the gap for several nucleotides and copy the opposite strand with one or more mismatched nucleotides to generate one or more mutations (3). The mismatch repair protein Msh2/6 may also bind the U–G mismatch. Following Msh2/6 recognition of the mismatch, other mismatch repair factors (not shown) catalyse removal of one strand; the strand harbouring a nearby nick, which in this case could be either strand, will be removed. In pathway 4, the G-containing strand is removed, leaving a U in single-stranded DNA that is efficiently removed by Ung. Mutations therefore can arise by DNA synthesis using the uninformative abasic site as a template, and/or by gap-filling by translesion polymerase(s). In pathway 5, the U-containing strand is removed, and mutations also could arise by gap-filling using translesion polymerase. REV1, a dCMP transferase, inserts a cytosine opposite abasic sites. Thus, REV1 can act in pathways 2 and 4 to generate C to G mutations at the original base deaminated by AID (6).