Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?

合作研究：海洋酸化是否会引起影响牡蛎下一代健康的甲基化反应？

• 批准号: 1634167
• 负责人: Steven Roberts
• 金额: $ 38.88万
• 依托单位: University of Washington
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-01-01 至 2021-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1634167&HistoricalAwards=false
• 关键词: Collaborative; Research; Does; ocean; acidification

Marine ecosystems worldwide are threatened by ocean acidification, a process caused by the unprecedented rate at which carbon dioxide is increasing in the atmosphere. Since ocean change is predicted to be rapid, extreme, and widespread, marine species may face an "adapt-or-die" scenario. However, modifications to the DNA sequence may be induced in response to a stress like ocean acidification and then inherited. Such "epigenetic" modifications may hold the key to population viability under global climate change, but they have been understudied. The aim of this research is to characterize the role of DNA methylation, a heritable epigenetic system, in the response of Eastern oysters (Crassostrea virginica) to ocean acidification. The intellectual merit lies in the integrative approach, which will characterize the role of DNA methylation in the intergenerational response of oysters to ocean acidification. These interdisciplinary data, spanning from molecular to organismal levels, will provide insight into mechanisms that underlie the capacity of marine invertebrates to respond to ocean acidification and lay the foundation for future transgenerational studies. Ocean acidification currently threatens marine species worldwide and has already caused significant losses in aquaculture, especially in Crassostrea species. This research has broader impacts for breeding, aquaculture, and the economy. Under the investigators' "Epigenetics to Ocean" (E2O) training program, the investigators will build STEM talent in bioinformatics and biogeochemistry, expose girls in low-income school districts to careers in genomics, and advance the field through open science and reproducibility. This research will specifically test if intermittent exposure to low pH induces a methylation response with downstream beneficial effects for biomineralization. These methylation states could be inherited and confer a fitness advantage to larvae that possess them. Phase 1 of the project will use an exposure experiment to determine the degree to which DNA methylation is altered and regulates the response to OA. Data from this experiment will be used to test the hypotheses that (i) DNA methylation, induced in the tissue of shell formation (i.e., mantle tissue), is correlated with changes in transcription and regulation of pallial fluid pH (calcifying fluid pH, measured by microelectrode), and (ii) that methylation changes induced in the mantle tissue are also induced in the germline --indicating that such changes are potentially heritable. Phase 2 of the project will use a pair-mated cross experiment to test the hypothesis that parental exposure to OA alters larval traits (calcification rate, shell structure, and polymorph mineralogy). Larvae will be generated from parents exposed to OA or control seawater, and then raised under control or OA conditions. Results will be used to (i) characterize inheritance of induced methylation states, (ii) estimate the variance in larval traits explained by genotype, non-genetic maternal/paternal effects, adult OA exposure, larval OA exposure, and parental methylome, and (iii) test the hypothesis that adult exposure alters the heritability (a quantity that predicts evolutionary response) of larval traits. Since the effects of epigenetic phenomena on estimates of heritability are highly debated, the results would advance understanding of this important issue. Because the investigators could discover that DNA methylation is a mechanism for heritable plastic responses to OA, knowledge of this mechanism would significantly improve and potentially transform predictive models for how organisms respond to global change.

全世界的海洋生态系统受到海洋酸化的威胁，海洋酸化是由二氧化碳在大气中增加的前所未有的速率引起的。由于预计海洋变化是快速，极端和广泛的，因此海洋物种可能面临“适应或饮食”的情况。但是，可以响应海洋酸化等应力，然后遗传而诱导对DNA序列的修饰。这种“表观遗传学”的修饰可能是全球气候变化下人口生存能力的关键，但已被研究了。这项研究的目的是表征一种可遗传的表观遗传系统DNA甲基化在东部牡蛎（Crassostrea Virginica）对海洋酸化的反应中的作用。智力优点在于综合方法，该方法将表征DNA甲基化在牡蛎对海洋酸化的代际反应中的作用。这些跨学科数据从分子到有机体水平，将洞悉海洋无脊椎动物对海洋酸化的能力的基础的机制，并为未来的转世研究奠定了基础。海洋酸化目前威胁着全球的海洋物种，并且已经在水产养殖中造成了重大损失，尤其是在泥泞的物种中。这项研究对繁殖，水产养殖和经济产生了更大的影响。在调查人员的“海洋表观遗传学”（E2O）培训计划下，研究人员将建立生物信息学和生物地球化学的STEM人才，使低收入学区的女孩揭露基因组学的职业，并通过开放的科学和可重复性提高领域。这项研究将特异性测试是否间歇性暴露于低pH值会诱导甲基化反应具有下游有益作用对生物矿化的作用。这些甲基化状态可以继承并赋予拥有它们的幼虫的健身优势。该项目的第1阶段将使用暴露实验来确定DNA甲基化改变的程度并调节对OA的反应。该实验的数据将用于检验假设，即（i）在壳形成组织中诱导的DNA甲基化（即地幔组织）与转录和调节的变化相关（钙化流体pH（钙化流体pH）（通过微电极pH测量）以及（ii）的生殖是甲基化的，该甲基化诱导的是梅壁细致的，该物质的变化是相关的。可能是可遗传的。该项目的第2阶段将使用成对的交叉实验来测试父母暴露于OA会改变幼虫特征（钙化率，壳结构和多晶型矿物学）的假设。幼虫将是由暴露于OA或控制海水的父母产生的，然后在控制或OA条件下饲养。 Results will be used to (i) characterize inheritance of induced methylation states, (ii) estimate the variance in larval traits explained by genotype, non-genetic maternal/paternal effects, adult OA exposure, larval OA exposure, and parental methylome, and (iii) test the hypothesis that adult exposure alters the heritability (a quantity that predicts evolutionary response) of larval traits.由于表观遗传现象对遗传力估计的影响是高度争议的，因此结果将提高人们对这一重要问题的理解。由于研究人员可以发现DNA甲基化是对OA的塑性反应的一种机制，因此对这种机制的了解将显着改善并有可能改变有机体对全球变化的反应的预测模型。

项目成果

General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica)

• DOI: 10.3389/fmars.2020.00225
• 发表时间: 2020-01
• 期刊: bioRxiv
• 作者: Yaamini R. Venkataraman;Alan M. Downey‐Wall;J. Ries;I. Westfield;S. White;S. Roberts;K. Lotterhos

Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases

无脊椎动物甲基化组提供了对环境耐受机制的深入了解并揭示了方法学偏差

• DOI: 10.1111/1755-0998.13542
• 发表时间: 2021
• 期刊: Molecular Ecology Resources
• 影响因子: 7.7
• 作者: Trigg, Shelly A.;Venkataraman, Yaamini R.;Gavery, Mackenzie R.;Roberts, Steven B.;Bhattacharya, Debashish;Downey‐Wall, Alan;Eirin‐Lopez, Jose M.;Johnson, Kevin M.;Lotterhos, Katie E.;Puritz, Jonathan B.
• 通讯作者: Puritz, Jonathan B.

Larval Response to Parental Low pH Exposure in the Pacific Oyster Crassostrea gigas

• DOI: 10.2983/035.038.0325
• 发表时间: 2019-12
• 期刊: Journal of Shellfish Research
• 影响因子: 1.3
• 作者: Yaamini R. Venkataraman;L. Spencer;S. Roberts