The Genetic Architecture of Somatic Mutation Rate

智力优势：DNA损伤非常重要，代价也足够高，以至于有机体需要投入大量基因来修复它，但人们对自然种群中个体潜在突变率的变化，或修复这些突变的能力的变化知之甚少。此外，对于这种变异的遗传决定因素的同一性，以及这些基因是否与实验室生物体研究中发现的基因不同，人们知之甚少。这一知识差距严重限制了理解维持基因组完整性的机制，以及理解依赖于突变的现象(如衰老)中的自然变异的能力。该项目的长期目标是了解影响自然界基因组稳定性的遗传和环境因素。该项目的中心假设是，个体的体细胞突变率不同，这种差异是由基因序列和基因表达的差异造成的。为了验证中心假设，该项目检测了来自北卡罗来纳州自然种群的40个近交系黑腹果蝇的体细胞突变率的变异。可获得这些品系的全基因组表达和序列数据。这项研究是通过最近创建的转基因模型来测量体内携带LacZ报告基因的果蝇的体细胞突变率而成为可能的。目的1通过在40个自交系中放置LacZ报告基因，并测量体细胞突变的品系、性别和组织特异性变异，来验证体细胞突变率存在遗传变异的假设。这一假设得到了初步数据的有力支持，这些数据表明体细胞突变率是可遗传的。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。单核苷酸多态的全基因组关联研究将用于识别与体细胞突变率相关的基因。将对表达数据进行分析，以寻找其表达水平与体细胞突变率相关的共同调控基因网络。目的3将确定自然高体细胞突变率的基因类型在暴露于百草枯时是否表现出相对较大的突变频率增加，百草枯是一种除草剂，已被证明能增加果蝇的突变频率。该项目创造性地结合了数量遗传学、分子遗传学和高通量基因组学。由于这项工作的重点是自然遗传变异，这项工作有望导致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。这一新的框架应该可以更好地理解基因组稳定性和基因组结构的演变。更广泛的影响：这项提议提供了对体细胞突变率的自然变异的第一个直接研究，并应导致识别与体细胞突变率相关的新基因。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提供持续的实践研究培训，包括来自代表性不足人群的学生。受训人员将有机会发表科学文章，并与调查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.