Investigating the landscape and genetic architecture of germline mutagenesis

项目摘要 DNA突变的速度最终决定了有多少人出生时患有严重的遗传疾病。 以及一个人在患癌症之前可能活多久。同样重要的是要了解 突变产生遗传变异，以便从基因组数据准确地推断进化历史。尽管 尽管基因突变对人类健康和疾病具有根本的重要性，但我们对基因突变率的变化知之甚少。 以及哪些遗传因素可能导致突变率的变化。我之前的研究 显示来自不同群体的突变偏向于发生在不同的序列背景中;例如， 欧洲人比非洲人或东亚人在“TCC”基序中含有更多的突变。这意味着，每个 群体受到序列偏倚突变过程的独特组合的影响。除非这些分歧- 结论都是由环境诱变剂引起的，其中一些必须是“增变等位基因”的标志， 遗传变异微妙地影响DNA损伤的可能性或DNA修复的效率。这项建议 描述了一个多管齐下的策略，询问DNA复制变异的原因和后果 忠诚第一步将是超越短的三个字母的基序，以确定较长的DNA序列， 种群间的变异性为了实现这一目标，我们将采用最近使用的统计技术， 来识别驱动免疫细胞超突变的基序。一旦我们确定了这些图案，我们将扫描它们， 与已知调节蛋白质结合和基因表达的丰富基序库一致。我们 旨在提高我们对突变率进化速度的理解，询问全球移民的作用 传播增变基因等位基因的事件，以及非遗传因素的贡献，如父母的年龄 效果在人类中，众所周知，母亲和父亲在怀孕时的年龄会影响 诱变的速率和谱，我们建议通过测序来更普遍地研究这种效应， 将年轻和年老的父母与他们的后代一起放在几种鱼类中，这是一种模式脊椎动物， 以成熟和衰老的速度而闻名。我们计划利用模式生物在另一个 在自然群体中，很难绘制突变等位基因的基因组位置，因为它们是 预测会迅速重组，远离他们创造的突变，但在实验室饲养的种群中，近亲繁殖可能会 用来迫使突变与它们产生的遗传背景保持联系。我们将开发方法 在两个不同的近交系模型系统中定位突变子等位基因：BXD重组近交系小鼠品系和 果蝇基因组参考小组，寻找特定遗传变异的基因组区域， 与特定序列上下文中的可变性相关。总之，这些研究路线将产生一个更全面的 诱变作为一种数量性状，在种群之间变化，并随着时间的推移而演变。

PROJECT SUMMARY The rate at which DNA mutates ultimately determines how many people are born with serious genetic dis- eases, as well as how long a person is likely to live before getting cancer. It is also crucial to understand how mutations generate genetic variation in order to accurately infer evolutionary history from genomic data. Despite this fundamental importance for human health and disease, we know little about how the mutation rate varies from person to person and what genetic factors might cause the mutation rate to vary. My previous research has shown that mutations from different populations are biased to occur in different sequence contexts; for example, Europeans contain more mutations in the motif “TCC” than Africans or East Asians do. This implies that each population is affected by a distinctive combination of sequence-biased mutational processes. Unless these dif- ferences are all induced by environmental mutagens, some of them must be the signatures of “mutator alleles,” genetic variants that subtly affect the likelihood of DNA damage or the efficacy of DNA repair. This proposal describes a multi-pronged strategy for interrogating the causes and consequences of variation in DNA replication fidelity. The first step will be to look beyond short, three-letter motifs to identify longer DNA sequences that differ in mutability between populations. To achieve this, we will adapt statistical techniques that have recently been used to identify the motifs that drive hypermutation in immune cells. Once we identify such motifs, we will scan them for concordance with the rich libraries of motifs that are known to regulate protein binding and gene expression. We aim to improve our understanding of the pace of mutation rate evolution, interrogating the role of global migration events in spreading mutator alleles, as well as the contribution of non-genetic factors such as the parental age effect. In humans, it is known that the ages of mothers and fathers at the time children are conceived impacts both the rate and spectrum of mutagenesis, and we propose to investigate this effect in greater generality by sequenc- ing young and old parents together with their offspring in a several species of killifish, a model vertebrate that is famous for maturing and aging extremely rapidly. We plan to exploit the utility of model organisms in another way as well: in natural populations, is difficult to map the genomic locations of mutator alleles because they are predicted to quickly recombine away from mutations they create, but in lab-reared populations, inbreeding can be used to force mutations to stay linked to the genetic backgrounds on which they arise. We will develop methods to map mutator alleles in two different inbred model systems: the BXD recombinant inbred mouse strains and the Drosophila Genome Reference Panel, looking for regions of the genome where specific genetic variants are associated with mutability in specific sequence contexts. Together, these lines of research will generate a fuller picture of mutagenesis as a quantitative trait that varies between populations and evolves over time.