EAGER proposal: Consequences of Environmental Stress-induced Epigenomes on Mutation and Organismal Fitness

突变是所有遗传变异的最终来源。因此，生物体如何与环境相互作用以影响产生突变的过程，对于理解所有进化变化的起源至关重要。科学家们正在迅速发现表观基因组的整合作用，表观基因组被定义为与DNA相互作用以修改基因功能的化合物，在介导环境和个体特征表达之间的反应中发挥作用。然而，这些环境控制的分子事件仍然几乎未知。本研究旨在表征环境诱导的表观遗传状态对突变频率，类型和遗传位置的影响，以更好地了解它们对生物体，种群和进化的健康和适应性的影响。水蚤，蚤状蚤，为这些研究提供了一个独特的机会，因为它是一个很好的建立环境压力的模型，其基因组是很好的特点，其生殖策略，包括克隆繁殖允许控制遗传和表观遗传背景。通过印第安纳州大学和芒特沙漠岛生物实验室的推广计划进行的这项研究将有利于年轻科学家的发展，特别是与本提案中将开发的新型生物信息学和计算方法有关的研究。通过这项研究获得的知识将对社会和人口的长期健康产生深远的影响，这些人在存在大量可以改变DNA的化学物质的情况下寿命更长。这项研究将利用现有的D。蚤属突变积累（MA）系在镉存在和不存在的情况下总共检查约10，000代并繁殖。镉在这里被用作模型环境应激源，因为它是一种强大的诱变剂，尽管不直接与DNA相互作用，它已被证明深刻影响遗传的染色质包装和DNA的表观遗传状态。然而，预计镉的表观遗传影响以及随后对突变的影响将在任何压力源中普遍存在。这些MA系已经进行了全基因组测序，建立了所有突变的谱（从头拷贝数变异、碱基取代突变和基因转换过程），在多代过程中量化了它们的适应性，并确定了突变对适应性的影响。本研究的目标是：1）通过鉴定来自单个MA系的染色质内的核小体占据来确定环境对DNA包装的影响，2）通过鉴定应激诱导的组蛋白翻译后修饰来表征应激对表观遗传状态的作用，以及3）研究表观遗传状态在调节对基因组的接近中所起的作用，从而增强突变，并影响生物体的健康。因此，这些研究将阐明表观基因组如何与基因组通信，以提供基因组和环境之间的接口。

Mutations are the ultimate source of all genetic variation. How organisms interact with the environment to influence the processes that generate mutations is therefore, critical for understanding the origin of all evolutionary change. Scientists are rapidly discovering the integrative role the epigenome, defined as chemical compounds that interact with DNA to modify gene function, plays in mediating responses between the environment and the expression of individual traits. However, the molecular events that underlie these environmentally governed controls remain virtually unknown. This research is designed to characterize the influence of environment induced epigenetic state on the frequency, types and genetic location of mutations to better understand their influence on the health and fitness of organisms, populations, and evolution. The waterflea, Daphnia pulex, offers a unique opportunity for these studies, because it is well established as a model of environmental stress, its genome is well characterized, and its reproductive strategy that includes clonal reproduction allows for control of both genetic and epigenetic background. This research through outreach programs at both Indiana University and Mount Desert Island Biological Laboratory will benefit the development of young scientist, especially related to the novel bioinformatics and computational approaches that will be developed in this proposal. The knowledge gained through this research stands to have profound implications for society and the long-term health of populations, which are living longer in the presence of a large diversity of chemicals that can modify DNA. This research will leverage preexisting D. pulex mutation accumulation (MA) lines bottlenecked ~10,000 total generations and propagated in the presence and absence of cadmium. Cadmium is used here as a model environmental stressor, because it is a powerful mutagen in spite of not interacting directly with DNA, and it has been shown to profoundly affect heritable chromatin packaging and epigenetic state of DNA. However, it is expected that the epigenetic affects due to cadmium and the subsequent influence on mutation will be generalizable across any stressor. These MA lines have already undergone whole genome sequencing, the spectra of all mutations (de novo copy number variants, base-substitution mutations, and gene conversion processes) are established, their fitness quantified over the course of multiple generations, and the mutational consequences on fitness determined. The goals of this research are to: 1) determine the environment's influence on DNA packaging by identifying nucleosome occupancy within chromatin from individual MA lines, 2) characterize the role of stress on epigenetic state by identifying stress induced post-translational modifications of histones, and 3) investigate the role epigenetic state plays in regulating access to the genome, thereby potentiating mutations, and influencing organismal fitness. Thus, these studies will elucidate how the epigenome communicates with the genome to provide an interface between the genome and the environment.