Rogozin et al.1 report that the WA motif is frequently mutated in V genes and that because pol η preferentially miscopies A and T in vitro, especially when the two nucleotides are in WA, it may play a role in hypermutation. In contrast, Dörner and Lipsky argue that pol η can only play a minor role because mutations occur more frequently in RGYW/WRCY than in WA. Two issues are being discussed here: first, is pol η involved in hypermutation of A and T and second, is the WA motif important? We have directly addressed these questions by examining mutations in V genes from three individuals with the variant form of the disease XP-V; these individuals did not express pol η, due to independent genetic defects2. If pol η is involved, the frequency of mutations of A and T should decrease in XP-V clones. This is indeed the case: only 15% of the total mutations occurred at A and T bases in XP-V clones (41 of 272) versus 45% in control clones (128 of 286). This marked shift in the mutational spectrum in XP-V clones implies that pol η participates in the hypermutation process.

Whether mutations occur in the WA motif is a separate issue. As Dörner and Lipsky point out, WA can be located within the RGYW/WRCY motifs and outside them. In our study, 17% of total mutations were in WA located in RGYW/WRCY in control clones versus 2% in XP-V clones; 11% of total mutations occurred in WA outside RGYW/WRCY in control clones versus 6% in XP-V clones; and 17% of total mutations were of A and T in non-WA motifs in control clones versus 7% in XP-V clones. This shows that in the absence of pol η, there was a lower frequency of A and T mutations, whether they were in WA sequences or not. The data support a model in which pol η preferentially miscopies A and T wherever they are found. This would happen in V genes because the pol has access to the template at the frequent strand breaks.

See Response 1 to 'Smaller role for pol η?' Igor B. Rogozinby, Somatic mutation hotspots correlate with DNA polymerase η error spectrum by Igor B. Rogozin, DNA polymerase η is an A-T mutator in somatic hypermutation of immunoglobulin variable genes by Xianmin Zeng and the Smaller role for pol η? by Thomas Dörner.