CURRENT FINDINGS USING L1 INSERTS TO DETERMINE THE FACTORS THAT AFFECT MUTATION RATE - The neutral DNA mutation rate (i.e., the accumulation of base substitutions in the absence of natural selection) is a fundamental biological parameter. Interestingly, it varies within and between chromosomes, but despite considerable study, this variation remains largely unexplained. For example, the neutral mutation rate varies with CpG content, a correlation thought to reflect the fact that the both are covariates of the genomic environment. However, by comparing the mutation rates of different L1 fossils we showed that CpGs per se, or mutations thereof, can directly affect the mutation of flanking non-CpG DNA( Walser, et al, Genome Res 18: 1403;Walser &Furano, Genome Res 20: 875). And an important result of this work was that a CpG content sufficient to affect non-CpG divergence also affects the mutational environment, producing transition/transversion ratios that are reminiscent of the "mutator phenotype" of some tumors. We therefore implemented an experimental system to directly determine in vivo whether DNA repair can induce mutations in flanking DNA and found that it does. In particular, the repair intermediates generated from preformed normally occurring DNA mispairs on an SV40-based episome were vulnerable at a low but statistically significant frequency to an APOBEC-mediated error-prone process. SiRNA knockdowns showed that components of both the base excision repair and mismatch repair pathways, or factors that can interact with these pathways (e.g., PCNA and ATR), and TpC-preferring APOBEC deaminases are all required for mutagenesis which produces mutations similar to those typical of the mutator phenotypes in various cancers. Thus normally error-free DNA repair processes can be turned into mutators providing a heretofore unexpected source of genetic changes that underlie disease, aging and evolutionary change. We have now submitted these results for publication.

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Chen, Jia; Furano, Anthony V (2015) Breaking bad: The mutagenic effect of DNA repair. DNA Repair (Amst) 32:43-51
Chen, Jia; Miller, Brendan F; Furano, Anthony V (2014) Repair of naturally occurring mismatches can induce mutations in flanking DNA. Elife 3:e02001
Walser, Jean-Claude; Furano, Anthony V (2010) The mutational spectrum of non-CpG DNA varies with CpG content. Genome Res 20:875-82
Walser, Jean-Claude; Ponger, Loic; Furano, Anthony V (2008) CpG dinucleotides and the mutation rate of non-CpG DNA. Genome Res 18:1403-14