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

突变是所有基因变异的最终来源。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综合作用，表观基因组被定义为与DNA相互作用以改变基因功能的化合物，在调节环境和个体特征表达之间的反应中发挥作用。然而，在这些环境控制之下的分子事件实际上仍然是未知的。本研究旨在描述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（Daphnia pulex）为这些研究提供了一个独特的机会，因为它被很好地确立为环境压力的模型，它的基因组被很好地表征，它的生殖策略包括无性繁殖，允许控制遗传和表观遗传背景。这项研究通过印第安纳大学和Mount Desert Island生物实验室的外展项目进行，将有利于年轻科学家的发展，特别是与本提案中开发的新型生物信息学和计算方法相关的研究。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，因为人们在存在多种可以修饰DNA的化学物质的情况下寿命更长。本研究将利用先前存在的D. pulex突变积累（MA）系瓶颈约10,000代，并在镉存在和不存在的情况下进行繁殖。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，尽管它不直接与DNA相互作用，它已被证明深刻影响遗传染色质包装和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应激源中普遍化。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、碱基替换突变和基因转换过程），在多代过程中量化了它们的适应度，并确定了突变对适应度的影响。本研究的目标是：1)通过鉴定单个MA系染色质内的核小体占用来确定环境对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；3)研究表观遗传状态在调节基因组通路，从而增强突变和影响有机体适应性方面的作用。因此，这些研究将阐明表观基因组如何与基因组沟通，以提供基因组与环境之间的接口。

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.