Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
, 10, 438
eCollection

Mutating for Good: DNA Damage Responses During Somatic Hypermutation

Affiliations
Review

Mutating for Good: DNA Damage Responses During Somatic Hypermutation

Bas Pilzecker et al. Front Immunol.

Abstract

Somatic hypermutation (SHM) of immunoglobulin (Ig) genes plays a key role in antibody mediated immunity. SHM in B cells provides the molecular basis for affinity maturation of antibodies. In this way SHM is key in optimizing antibody dependent immune responses. SHM is initiated by targeting the Activation-Induced Cytidine Deaminase (AID) to rearranged V(D)J and switch regions of Ig genes. The mutation rate of this programmed mutagenesis is ~10-3 base pairs per generation, a million-fold higher than the non-AID targeted genome of B cells. AID is a processive enzyme that binds single-stranded DNA and deaminates cytosines in DNA. Cytosine deamination generates highly mutagenic deoxy-uracil (U) in the DNA of both strands of the Ig loci. Mutagenic processing of the U by the DNA damage response generates the entire spectrum of base substitutions characterizing SHM at and around the initial U lesion. Starting from the U as a primary lesion, currently five mutagenic DNA damage response pathways have been identified in generating a well-defined SHM spectrum of C/G transitions, C/G transversions, and A/T mutations around this initial lesion. These pathways include (1) replication opposite template U generates transitions at C/G, (2) UNG2-dependent translesion synthesis (TLS) generates transversions at C/G, (3) a hybrid pathway comprising non-canonical mismatch repair (ncMMR) and UNG2-dependent TLS generates transversions at C/G, (4) ncMMR generates mutations at A/T, and (5) UNG2- and PCNA Ubiquitination (PCNA-Ub)-dependent mutations at A/T. Furthermore, specific strand-biases of SHM spectra arise as a consequence of a biased AID targeting, ncMMR, and anti-mutagenic repriming. Here, we review mammalian SHM with special focus on the mutagenic DNA damage response pathways involved in processing AID induced Us, the origin of characteristic strand biases, and relevance of the cell cycle.

Keywords: DNA damage tolerance (DDT); abasic site; base excision repair; cytosine deamination; non-canonical mismatch repair (ncMMR); translesion synthesis (TLS).

Figures

Figure 1
Figure 1
Mutagenic pathways of SHM. Deamination of C by AID during SHM leads to a specific mutagenic spectrum. The creation of the full SHM spectrum depends on (1) replication opposite template U instructs a template T and generates transitions at C/G. (2) UNG2 dependent TLS generates C/G transversions. UNG2 converts a U into an abasic site. As abasic sites are non-instructive, TLS opposite these sites generates both transitions and transversions. (3) Hybrid pathway between non-canonical mismatch repair (ncMMR) and UNG2 dependent TLS generates transversions at C/G. (4) ncMMR generates the majority of mutations at A/T. (5) UNG2- and PCNA Ubiquitination (PCNA-Ub)- dependent mutations at A/T. This non-canonical long-patch BER pathway generates a minor but significant subset of A/T mutations (~8%).
Figure 2
Figure 2
Detailed model of ncMMR in A/T mutagenesis. After U induction by AID, UNG2 processes U into an abasic site. In this more detailed model of ncMMR there are to arm on ncMMR, (1) UNG2 and APEX2 provide the incision for EXO1. EXO1 requires MSH2/6 and a 5' gap to the mismatch to be generate single-stranded DNA. PCNA-Ub recruits POLH, which can fill in the single-stranded DNA gap. (2) MSH2/MSH6 complex recognizes mismatch and activate the PMS2/MLH1 complex to make the incision. EXO1 creates singles stranded DNA gap, which is filled in by POLH.
Figure 3
Figure 3
Strand-biases in SHM. (A) AID targeting with a preference for the coding strand leads to a C/G transition strand bias. Us on the coding strand lead to C>T transitions, while Us on the non-coding strand lead to a G>A transitions. (B) During error-prone mismatch repair, the MSH2/MSH6 complex recognizes the U-G mismatch, after which APEX2 or PMS2 provide the incisions for EXO1. POLH is especially error-prone on template TW. Therefore, the orientation of the gap made by EXO1 likely governs the A/T bias. (C) Replicative forks can be stalled on both leading and lagging strand by AID dependent abasic sites (1). After priming on the lagging strand, a replicative polymerase resumes DNA synthesis. PRIMPOL establishes G>C over C>G transversion bias found in Jh4 intron of the Igh gene, likely though anti-mutagenic activity on the leading strand of replication. PRIMPOL restarts by repriming after stalled DNA synthesis (2) and prevents TLS (3). On the lagging strand, TLS opposite of the abasic site leads to G>C mutations (4). PRIMPOL activity likely activates a homology driven error-free pathway such as template switching to prevent mutagenesis (5). (C) adapted from Pilzecker et al. (73).
Figure 4
Figure 4
The potential but unlikely role of pre/mRNA in A/T mutagenesis. As the pre/mRNA is copied from the non-coding strand, it can only act as template for repair synthesis on the non-coding strand. After the pre/mRNA is copied from the non-coding strand, a gap can arise in the DNA-RNA hybrid on the non-coding DNA strand. As POLH has reverse transcriptase activity, this gap will be filled in an error-prone manner by POLH. However, if this potential mechanism or any other mechanism using the cDNA as an intermediate would be a dominant mode, a higher rate of T mutations compared to A mutations is expected, which directly contrasts the observed A/T bias.

Similar articles

See all similar articles

Cited by 4 PubMed Central articles

References

    1. Neuberger MS, Milstein C. Somatic hypermutation. Curr Opin Immunol. (1995) 7:248–54. 10.1016/0952-7915(95)80010-7 - DOI - PubMed
    1. Storb U, Peters A, Kim N, Shen HM, Bozek G, Michael N, et al. . Molecular aspects of somatic hypermutation of immunoglobulin genes. Cold Spring Harb Sympos Quant Biol. (1999) 64:227–34. 10.1101/sqb.1999.64.227 - DOI - PubMed
    1. Kinoshita K, Honjo T. Linking class-switch recombination with somatic hypermutation. Nat Rev Mol Cell Biol. (2001) 2:493–503. 10.1038/35080033 - DOI - PubMed
    1. Papavasiliou FN, Schatz DG. Somatic hypermutation of immunoglobulin genes: merging mechanisms for genetic diversity. Cell. (2002) 109(Suppl.) S35–44. - PubMed
    1. Seki M, Gearhart PJ, Wood RD. DNA polymerases and somatic hypermutation of immunoglobulin genes. EMBO Rep. (2005) 6:1143–8. 10.1038/sj.embor.7400582 - DOI - PMC - PubMed
Feedback