The Genetic Architecture of Somatic Mutation Rate

智力优点：DNA损伤非常重要，而且代价高昂，以至于生物体需要大量的基因来修复它，但人们对自然种群中的个体在潜在突变率或修复这些突变的能力方面的差异知之甚少。此外，很少有人了解这种变异的遗传决定因素的身份，以及这些基因是否与实验室生物研究中发现的基因不同。这种知识上的差距严重限制了理解维持基因组完整性的机制的能力，以及理解衰老等依赖突变的现象中的自然变异的能力。该项目的长期目标是了解自然界中影响基因组稳定性的遗传和环境因素。该项目的中心假设是，个体在体细胞突变率方面存在差异，并且这种差异是由基因序列和基因表达的差异引起的。为了验证中心假设，本项目研究了来自北卡罗来纳州自然种群的40个黑腹果蝇近交系的体细胞突变率的变化。这些品系的全基因组表达和序列数据是可用的。这项研究是可能的，最近建立了一个转基因模型，以测量体细胞突变率在体内的果蝇与lacZ报告基因。目的1将涉及实验，以测试的假设，即遗传变异存在的体细胞突变率放置一个lacZ报告基因到40个近交系和测量线，性别和组织特异性变异体细胞突变。这一假说得到了初步数据的有力支持，这些数据显示了体细胞突变率的遗传变异。在目标2中，将研究与体细胞突变率相关的遗传和调控因素。单核苷酸多态性的全基因组关联研究将用于鉴定与体细胞突变率相关的基因。将分析表达数据以搜索其表达水平与体细胞突变率相关的共调节基因的网络。目标3将确定具有天然高体细胞突变率的基因型在接触百草枯时是否显示出相对较大的突变频率增加，百草枯是一种除草剂，先前已显示出增加果蝇突变频率。该项目使用了数量遗传学，分子遗传学和高通量基因组学的创造性组合。在其对自然遗传变异的关注中，这项工作有望发现影响体细胞突变率进化相关变异的新基因，并为理解体细胞突变率的遗传基础创造一个新的范式。这个新的框架应该提供更好的理解基因组稳定性和基因组结构的演变。 更广泛的影响：这一建议提供了第一个直接的研究自然变异的体细胞突变率，并应导致识别新的基因与体细胞突变率。在该项目过程中开发的所有新菌株和收集的所有表达数据将免费提供给研究界。该项目将为高中生和本科生（包括来自代表性不足群体的学生）提供持续的实践研究培训。受训人员将有机会发表科学文章，并与研究人员一起参加国家科学会议。

Intellectual merit: DNA damage is important and costly enough that organisms devote scores of genes to its repair, but little is known about how individuals in natural populations vary in their underlying mutation rates, or in their ability to repair those mutations. Furthermore, little is understood about the identity of the genetic determinants of this variation, and whether these genes differ from those found in studies on laboratory organisms. This gap in knowledge seriously limits the ability to understand the mechanisms that maintain genome integrity, and to understand natural variation in mutation-dependent phenomena such as senescence. The long-term goal of this project is to understand the genetic and environmental factors that affect genome stability in nature. The central hypothesis of this project is that individuals vary in somatic mutation rate, and that this variation is caused by differences in gene sequences and gene expression. To test the central hypothesis, this project examines variation in somatic mutation rate in 40 inbred lines of Drosophila melanogaster derived from a natural population in North Carolina. Genome-wide expression and sequence data are available for these lines. The study is made possible by the recent creation of a transgenic model to measure somatic mutation rates in vivo in the fruit fly with a lacZ reporter gene. Aim 1 will involve experiments to test the hypothesis that genetic variation exists for somatic mutation rate by placing a lacZ reporter gene into the 40 inbred lines and measuring line-, sex- and tissue-specific variation for somatic mutation. This hypothesis is strongly supported by preliminary data showing heritable variation for somatic mutation rate. In Aim 2, genetic and regulatory factors associated with somatic mutation rate will be investigated. Genome-wide association studies of single nucleotide polymorphisms will be used to identify genes associated with somatic mutation rate. Expression data will be analyzed to search for networks of co-regulated genes whose expression levels correlate with somatic mutation rate. Aim 3 will determine whether genotypes with naturally high somatic mutation rate show relatively large increases in mutation frequency when exposed to paraquat, a herbicide that has been shown previously to increase the frequency of mutations in Drosophila. This project uses a creative combination of quantitative genetics, molecular genetics, and high-throughput genomics. In its focus on natural genetic variation, this work is expected to lead to the discovery of new genes that influence evolutionarily relevant variation in somatic mutation rates and to create a novel paradigm for understanding the genetic basis of somatic mutation rate. This new framework should provide better understanding of the evolution of genome stability and genome structure. Broader impacts: This proposal provides the first direct study of natural variation for somatic mutation rate, and should lead to the identification of novel genes associated with somatic mutation rate. All novel strains developed and all expression data collected during the course of this project will be made freely available to the research community. The project will provide continued hands-on research training for high school and undergraduate students, including students from underrepresented populations. Trainees will be given the opportunity to publish scientific articles and to attend national scientific meetings with the investigator.