Mammalian L1 retrotransposons as genetic characters

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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). We now find that the effect of CpG content on non-CpG mutations requires a certain threshold to have an observable effect and that it also reaches "saturation". Most provocatively, changes in the non-CpG mutation rate are paralleled by changes in the mutational spectrum. Thus, 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 implemented an efficient experimental system to directly examine the effect of DNA mutations at both CpGs and non-CpG sites on the mutation of flanking non modified DNA in vivo. We found that DNA mutations can indeed affect the mutation rate at normal flanking DNA and are now determining the mechanism by which this effect occurs. We are also determining the effect of other DNA modifications on the mutation rate of flanking non-modified DNA as well as which DNA repair pathways are involved and whether DNA replication also plays a role in these processes. We are now preparing for publication the first phase of this study.