Rapid cell division contributes to efficient induction of A/T mutations during Ig gene hypermutation

Development and Longevity: Cellular and Molecular Determinants - A Mini-Review

Across species, development and longevity are tightly linked. We discuss the relevant literature and suggest that the root for this stringent relationship is the rate of development. The basis for the relationship between rate of development and longevity lies in adaptations that have occurred through evolution at multiple levels of biological complexity: organism, organ, cellular, and molecular. Thus, the analysis of the relationship is of interest for multiple fields of biology.

JH6 downstream intronic sequence is dispensable for RNA polymerase II accumulation and somatic hypermutation of the variable gene in Ramos cells

Activation-induced deaminase (AID) introduces nucleotide substitutions within the variable region of immunoglobulin genes to promote antibody diversity. This activity, which is limited to 1.5 kb downstream of the variable gene promoter, mutates both the coding exon and downstream intronic sequences. We recently reported that RNA polymerase II accumulates in these regions during transcription in mice. This build-up directly correlates with the area that is accessible to AID, and manipulation of RNA polymerase II levels alters the mutation frequency. To address whether the intronic DNA sequence by itself can regulate RNA polymerase II accumulation and promote mutagenesis, we deleted 613 bp of DNA downstream of the J_H6 intron in the human Ramos B cell line. The loss of this sequence did not alter polymerase abundance or mutagenesis in the variable gene, suggesting that most of the intronic sequence is dispensable for somatic hypermutation.

DNA polymerases β and λ do not directly affect Ig variable region somatic hypermutation although their absence reduces the frequency of mutations

During somatic hypermutation (SHM) of antibody variable (V) region genes, activation-induced cytidine deaminase (AID) converts dC to dU, and dUs can either be excised by uracil DNA glycosylase (UNG), by mismatch repair, or replicated over. If UNG excises the dU, the abasic site could be cleaved by AP-endonuclease (APE), introducing the single-strand DNA breaks (SSBs) required for generating mutations at A:T bp, which are known to depend upon mismatch repair and DNA Pol η. DNA Pol β or λ could instead repair the lesion correctly. To assess the involvement of Pols β and λ in SHM of antibody genes, we analyzed mutations in the VDJh4 3' flanking region in Peyer's patch germinal center (GC) B cells from polβ(-/-)polλ(-/-), polλ(-/-), and polβ(-/-) mice. We find that deficiency of either or both polymerases results in a modest but significant decrease in V region SHM, with Pol β having a greater effect, but there is no effect on mutation specificity, suggesting they have no direct role in SHM. Instead, the effect on SHM appears to be due to a role for these enzymes in GC B cell proliferation or viability. The results suggest that the BER pathway is not important during V region SHM for generating mutations at A:T bp. Furthermore, this implies that most of the SSBs required for Pol η to enter and create A:T mutations are likely generated during replication instead. These results contrast with the inhibitory effect of Pol β on mutations at the Ig Sμ locus, Sμ DSBs and class switch recombination (CSR) reported previously. We show here that B cells deficient in Pol λ or both Pol β and λ proliferate normally in culture and undergo slightly elevated CSR, as shown previously for Pol β-deficient B cells.

High levels of AID cause strand bias of mutations at A versus T in Burkitt's lymphoma cells

Ig gene somatic hypermutation in the germinal center (GC) B cells occurs at C and G at roughly the same frequency. In contrast, there is a 2-fold increase of mutations at A relative to T on the non-transcribed strand of the V genes but it is unclear what triggers such strand bias. Using an efficient mutagenesis system that recapitulates characteristic features of Ig gene hypermutation in the GC B cells, we found that low levels of AID induced similar frequency of mutations at A and T. However, high levels of AID specifically increased mutations at A, but not T, leading to strand bias. These results explain why strand bias of A:T mutations is observed only in the highly mutated V genes but not in the less mutated switch region or the BCL-6 gene. High levels of AID also increased the proportion of transversions at G relative to transversions at C. Our results identify a clue to the strand bias of A:T mutations and provide an in vitro model to elucidate this unsolved mystery in the hypermutation field.

Analysis of Ig gene hypermutation in Ung(-/-)Polh(-/-) mice suggests that UNG and A:T mutagenesis pathway target different U:G lesions

The activation-induced cytidine deaminase (AID) initiates Ig gene hypermutation by converting cytosine to uracil (U) and generating a U:G lesion. Genetic and biochemical studies suggest that the AID-triggered U:G lesions are processed by three mutagenic pathways to induce mutations at both C:G and A:T pairs. First, direct replication of the U:G lesion leads to C to T and G to A transitions. Second, U can be excised by the uracil DNA glycosylase (UNG) and the replication/processing of the resulting abasic site leads to transversions and transitions at C:G pairs. Third, the U:G lesion is recognized by an atypical mismatch repair (MMR) pathway which generates mutations at A:T pairs in a DNA polymerase η (POLH)-dependent manner. To further explore whether these three mutagenic pathways function competitively or independently, we have analyzed Ig gene hypermutation in mice deficient in both UNG and POLH. Compared with WT mice, UNG deficiency caused elevated frequency of C:G mutations, suggesting that UNG-mediated U excision led to error-free as well as error-prone repair. In contrast, UNG deficiency did not affect the frequency and patterns of A:T mutations, suggesting that the MMR did not target U:G lesions normally recognized and processed by UNG. In addition, POLH deficiency did not affect the frequency and patterns of C:G mutations and UNG POLH double deficiency showed an additive effect of single deficiency. Based on these observations and previous results, along with the recent finding that UNG excises AID-triggered U predominantly during G1 phase of the cell cycle, it appears that UNG and MMR targets U:G lesions generated during G1 and S phases of the cell cycle, respectively.