Repair of naturally occurring mismatches can induce mutations in flanking DNA

Abstract

‘Normal’ genomic DNA contains hundreds of mismatches that are generated daily by the spontaneous deamination of C (U/G) and methyl-C (T/G). Thus, a mutagenic effect of their repair could constitute a serious genetic burden. We show here that while mismatches introduced into human cells on an SV40-based episome were invariably repaired, this process induced mutations in flanking DNA at a significantly higher rate than no mismatch controls. Most mutations involved the C of TpC, the substrate of some single strand-specific APOBEC cytidine deaminases, similar to the mutations that can typify the ‘mutator phenotype’ of numerous tumors. siRNA knockdowns and chromatin immunoprecipitation showed that TpC preferring APOBECs mediate the mutagenesis, and siRNA knockdowns showed that both the base excision and mismatch repair pathways are involved. That naturally occurring mispairs can be converted to mutators, represents an heretofore unsuspected source of genetic changes that could underlie disease, aging, and evolutionary change.

DOI: http://dx.doi.org/10.7554/eLife.02001.001

eLife digest

The inherent chemical instability of the four bases that are found in DNA leads to our genetic material being damaged on a daily basis. The sequence of these bases codes the genetic instructions necessary for all cellular functions, so damaged bases must be efficiently recognized and accurately repaired. The base excision repair pathway carries out these functions.

However, there are some circumstances in which random changes to the genetic code can be beneficial. In immune cells, for example, these changes enhance the diversity of antibodies generated to fight bacteria and viruses. In immune cells, a second repair pathway—the mismatch repair pathway—hijacks the base excision repair pathway. This gives enzymes belonging to the APOBEC family access to the DNA that is undergoing repair, and these enzymes change cytosine bases to uracil bases. Subsequent processing steps can lead to different bases substituted for the original cytosine. The recent discovery that APOBEC enzymes are abundant in other types of cells raised the possibility that these enzymes could be significant source of mutations in the DNA of cells where such mutations are not welcome.

To explore this possibility Chen et al. deliberately introduced a number of mutations (that are normally repaired by the base excision repair pathway) into non-immune human cells and observed what happened. The mutations were repaired, but the number of mutations in neighboring bases increased by a statistically significant amount. In particular, most of these mutations involved a cytosine base that was preceded by a thymine base. Chen et al. also showed that both APOBEC and the mismatch repair pathway are involved, as is the case for the mutations caused by APOBEC enzymes in immune cells. Similar APOBEC mutations are known to be involved in cancer.

The model system developed by Chen et al. not only shows that normally error-free DNA repair can be involved in generating these mutations, but also used to obtain a better understanding of these processes and thereby provide new insights in cancer biology.

DOI: http://dx.doi.org/10.7554/eLife.02001.002