Hypermutation at A-T Base Pairs: The A Nucleotide Replacement Spectrum Is Affected by Adjacent Nucleotides and There Is No Reverse Complementarity of Sequences Flanking Mutated A and T Nucleotides

Abstract

Hypermutation is thought to be a two-phase process. The first phase is via the action of activation-induced cytidine deaminase (AID), which deaminates C nucleotides in WRC motifs. This results in the RGYW/WRCY hot spot motifs for mutation from G and C observed in vivo. The resemblance between the hot spot for C mutations and the reverse complement of that for G mutations implies a process acting equally on both strands of DNA. The second phase of hypermutation generates mutations from A and T and exhibits strand bias, with more mutations from A than T. Although this does not concur with the idea of one mechanism acting equally on both strands, it has been suggested that the AT mutator also has a reversible motif; WA/TW. We show here that the motifs surrounding the different substitutions from A vary significantly; there is no single targeting motif for all A mutations. Sequence preferences associated with mutations from A more likely reflect an influence of adjacent nucleotides over what the A mutates “to.” This influence tends toward “like” replacements: Purines (A or G) in the 5′ position bias toward replacement by another purine (G), whereas replacement with pyrimidines (C or T) is more likely if the preceding base is also a pyrimidine. There is no reverse complementarity in these observations, in that similar influences of nucleotides adjacent to T are not seen. Hence, WA and TW should not be considered as reverse complement hot spot motifs for A and T mutations.

Ectopic GC in the thymus of myasthenia gravis patients show characteristics of normal GC

“…Indeed, the analysis of lineage tree properties showed no significant differences between the MG and the normal GC trees, despite the chronic nature of the response, suggesting that the diversification, selection and mutation processes that take place in these ectopic GC are similar to normal responses. In agreement with this, SHM targeting motifs of the IF and OOF MG sequences were similar to the normal GC sequences, exhibiting the motifs reported in the literature [11,17,18,[23][24][25]. However, the MG IF Ig gene rearrangements exhibited a slight transversion bias that proved to be significantly different compared with the normal IF group.…”

“…MG, myasthenia gravis, IF, in frame and OOF, out-of-frame. whereas mutations from A and T occur in WA/TW motifs [11,17,18,[23][24][25]. We next examined whether nucleotides were mutated around these motifs and in the same positions that are reported in the literature in the MG and the normal GC groups.…”

“…Mutation spectrum Studies concerning the somatic hypermutation (SHM) spectrum show that normally, mutations from C/G base pairs are mutated with a similar frequency in reverse complement motifs, implying that the SHM machinery acts equally on both DNA strands [11][12][13][14][15][16][17][18][19][20]]. However, A is usually more frequently mutated than T, suggesting that there is a bias for generating these mutations on only one strand, during the second phase of SHM [11,16,[20][21][22].…”

Overlapping hotspots in CDRs are critical sites for V region diversification

“…In addition, there are more WA Polη hotspots in CDR1 and CDR2 than in FW1 and FW2. Approximately 45% of the A:T residues in CDR1 and CDR2 are in Polη hotspots, and most of these are in TA motifs, which are more susceptible to errors (50)(51)(52), whereas in FW1 and FW2, the percentage of A:T residues that are in TA motifs is much lower (Fig. S2B).…”

Lineage tree analysis of high throughput immunoglobulin sequencing clarifies B cell maturation pathways

“…Mutation targeting motif analysis was based on previous work by Dunn-Walters et al [48] [49]. Briefly, the base composition at positions flanking a mutation (ten nucleotides on either side) was determined.…”