AID-generated somatic hypermutations affect the variable (V) regions of genes encoding immunoglobulins. SHM is restricted to VDJ regions and their adjacent flanks in immunoglobulin (Ig) genes, whereas constant regions are spared because AID does not gain access to the 5' and constant regions of Ig genes.[r1] Mutations occur after about 100 nucleotides downstream of the promoter and extend to 1-2 kb. Somatic (hyper)mutation affects only individual cells of the immune system, so the programmed mutations that it generates are transmitted only within the particular cell line (somatic) and are not transmitted to the organism's offspring.
Following activation of naïve B cells and during the subsequent antigen-stimulated proliferation of B cells, the gene locus for the Ig-BCR experiences a highly accelerated rate of somatic mutation (increased by a factor of 10^5 to 10^6). This acceleration is attributable to the enzyme activation-induced (cytidine) deaminase (AID), which extracts the amino group from a deoxycytidine base in DNA, converting deoxycytidine to deoxyuracil. Deoxycytidine is a nucleoside formed through attachment of the nucleobase cytosine to a deoxyribose ring via a β-N1-glycosidic bond, and deamination of cytosine generates uracil in deoxyuridine (dUMP) im C to U.
AID-catalyzed deamination of deoxycytidine creates a single nucleotide polymorphism (SNP) in the DNA strand by generating a uracil:guanine mismatch. The nucleobases that normally occur in DNA are adenine paired with thymine, and cytosine paired with guanine. Uracil is normally found only in RNA, where it is paired with adenine.
A high-fidelity base excision repair enzyme, uracil-DNA glycosylase (UNG2), excises the alien uracil nucleobase, then error-prone DNA polymerases complete the base-excision repair. During this base-excision repair, incorrect nucleobases may be substituted at or adjacent to the original C to U mutation site. Mispairing (transition) mutations are susceptible to indels - insertions and deletions. (Such mutation vulnerable areas in the genome are termed 'hotspots', and they have played a significant role in biological evolution.)
Thus, while AID deamination generates mutagenic U:G mismatches, DNA-incorporated dUMP generates U:A pairs that are not directly mutagenic, but which may be cytotoxic. Usually, deleterious mutations that could result from uracil withiin DNA are prevented by error-free base excision repair.
However, B-cells employ uracil in DNA as a physiological intermediate in the somatic hypermutation processes that promote secondary antibody diversification in adaptive immunity. Here, activation-induced cytosine deaminase (AID) introduces template uracils that provide for GC to AT transition mutations at the Ig locus after replication. When the base excision repair enzyme uracil-DNA glycosylase (UNG2) excises uracil, error-prone DNA polymerases may causes other mutations at/near the abasic site of the Ig locus.
Together, these processes are central to the somatic hypermutation (SHM) mechanism that increases immunoglobulin diversity. Similarly, AID and UNG2 are also essential for the generation of strand breaks that initiate the process of class-switch recombination (CSR).
[r1] The very 5' end and the constant region of Ig genes are spared from somatic mutation because AID does not access these regions. Longerich S, Tanaka A, Bozek G, Nicolae D, Storb U. J Exp Med. 2005 Nov 21;202(10):1443-54. [Free Full Text Article]