Mammalian L1 retrotransposons as genetic characters

使用L1插入来确定影响突变率的因素-中性DNA突变率(即在没有自然选择的情况下碱基替换的积累)是一个基本的生物学参数。有趣的是，它在染色体内和染色体之间有所不同，但尽管进行了大量研究，这种差异在很大程度上仍然无法解释。例如，中性突变率随着CpG含量的不同而变化，这种相关性被认为反映了两者都是基因组环境的协变量的事实。然而，通过比较不同L1化石的突变率，我们发现CPGS本身或其突变可以直接影响侧翼非CpG DNA的突变(Walser等人，Genome 18：1403；Walser&Furano，Genome 20：875)。我们现在发现，CpG含量对非CpG突变的影响需要一定的阈值才能产生可观察到的效果，而且它也达到了“饱和”。最具挑衅性的是，非CpG突变率的变化与突变谱的变化是平行的。因此，足以影响非CpG分歧的CpG含量也会影响突变环境，产生的转换/颠换比率使人想起某些肿瘤的“突变子表型”。我们建立了一个有效的实验系统，在体内直接检测CpGS和非CpG位点的DNA突变对非修饰DNA侧翼突变的影响。我们发现DNA突变确实可以影响正常DNA侧翼的突变率，现在正在确定这种影响发生的机制。我们还在确定其他DNA修饰对未修饰DNA侧翼突变率的影响，以及涉及哪些DNA修复途径，以及DNA复制是否也在这些过程中发挥作用。我们现在已经完成了关于这个主题的第一份手稿，我们很快就会提交出版。

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 have now completed our first manuscript on this topic, which we will be submitting for publication soon.