Investigating the landscape and genetic architecture of germline mutagenesis

研究种系突变的景观和遗传结构

• 批准号: 10453732
• 负责人: Kelley Harris
• 金额: $ 40.31万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-07 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10453732
• 关键词: Affect; African; Age; Alleles; Animal Model; Binding Proteins; Biological Models; Cells; Complement; DNA; DNA Damage; DNA Repair; DNA Sequence; DNA Sequence Alteration; DNA biosynthesis; Disease; Drosophila genome; East Asian; European; Event; Evolution; Gene Expression; Genetic; Genetic Diseases; Genetic Variation; Genome; Genomics; Health; Human; Hybrids; Immune; Inbred Strains Mice; Inbreeding; Individual; Letters; Libraries; Link; Location; Malignant Neoplasms; Maps; Methods; Migrant; Mutagenesis; Mutate; Mutation; Persons; Play; Polar Bear; Population; Process; Recombinants; Recording of previous events; Research; Role; Scanning; Techniques; Time; Ursidae Family; Variant; Work; environmental mutagens; genetic architecture; genetic variant; genomic data; improved; innovation; offspring; reference genome; trait

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. For the first time, we propose to incorporate ancient DNA into our analyses of human mutation spectrum variation, aiming to improve our understanding of the pace of mutation rate evolution and interrogate the role of global mi- gration events in spreading mutator alleles. As a complement to this work on humans, we will also study mutation sequence context variation in polar bears and brown bears, which have been hybridizing for thousands of years in a unidirectional way with polar bear migrants entering the brown bear population but never the reverse. By analyzing the covariance of mutational sequence context in polar bears and brown bears across a range of allele ages, we will infer how often mutator alleles have crossed from one species to another. 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; to overcome this difficulty, we are working with collaborators to study mutagenesis in model organisms, where 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.

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 尽管突变率对人类健康和疾病至关重要，但我们对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。为 第一次，我们建议将古代DNA纳入我们对人类突变谱变异的分析中， 旨在提高我们对突变率进化速度的理解，并询问全局MI的作用， 扩散增变基因等位基因的进化事件。作为对人类研究的补充，我们还将研究突变 北极熊和棕熊的序列背景变异，它们已经杂交了数千年 北极熊移民进入棕熊种群的单向方式，但从来没有相反。通过 分析北极熊和棕熊在一系列等位基因中突变序列背景的协方差 年龄，我们将推断增变基因等位基因从一个物种到另一个物种的频率。在自然种群中， 很难绘制增变基因等位基因的基因组位置，因为它们被预测会迅速重组， 为了克服这一困难，我们正在与合作者合作研究诱变， 在模式生物中，近亲繁殖可以用来迫使突变与遗传背景保持联系， 他们所产生的。我们将开发在两种不同的近交系模型系统中定位增变基因等位基因的方法： BXD重组近交系小鼠品系和果蝇基因组参考组，寻找基因组的区域。 基因组，其中特定的遗传变异与特定序列背景下的突变性相关。在一起， 这些研究路线将产生一个更全面的图片诱变作为一个数量性状， 随着时间的推移，人口和进化。