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

全世界的海洋生态系统都受到海洋酸化的威胁，这一过程是由大气中二氧化碳以前所未有的速度增加造成的。由于海洋变化预计将是迅速、极端和广泛的，海洋物种可能面临“要么适应，要么死亡”的局面。然而，DNA序列的改变可能是对海洋酸化等压力的反应，然后遗传。这种“表观遗传”修饰可能是全球气候变化下人口生存能力的关键，但对它们的研究还不够充分。本研究的目的是表征DNA甲基化（一种可遗传的表观遗传系统）在东方牡蛎（Crassostrea virginica）对海洋酸化的反应中的作用。智力上的优点在于综合方法，它将描述DNA甲基化在牡蛎对海洋酸化的代际反应中的作用。这些跨学科的数据，从分子水平到有机体水平，将提供深入了解海洋无脊椎动物对海洋酸化反应能力的机制，并为未来的跨代研究奠定基础。海洋酸化目前威胁着世界各地的海洋物种，并已经造成水产养殖的重大损失，特别是在长牡蛎物种中。这项研究对养殖、水产养殖和经济有更广泛的影响。根据研究人员的“从表观遗传学到海洋”（E2O）培训计划，研究人员将培养生物信息学和生物地球化学方面的STEM人才，让低收入学区的女孩接触基因组学的职业，并通过开放科学和可重复性推进该领域的发展。本研究将专门测试间歇性暴露于低pH是否会诱导甲基化反应，并对下游生物矿化产生有益影响。这些甲基化状态可以遗传，并赋予具有它们的幼虫适应性优势。该项目的第一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验证以下假设：(i)在壳形成组织（即套膜组织）中诱导的DNA甲基化与白质液pH值（通过微电极测量的钙化液pH值）的转录和调节变化相关，以及（ii）在套膜组织中诱导的甲基化变化也在种系中诱导-表明这种变化可能是可遗传的。该项目的第二阶段将使用配对交叉实验来验证亲代接触OA会改变幼虫特征（钙化率、壳结构和多态矿物学）的假设。幼虫将由接触OA或对照海水的亲本产生，然后在对照或OA条件下饲养。结果将用于(i)表征诱导甲基化状态的遗传特征，（ii）估计由基因型、非遗传母本/父本效应、成年OA暴露、幼虫OA暴露和亲本甲基组解释的幼虫性状的差异，以及（iii）检验成年暴露改变幼虫性状的遗传力（预测进化反应的数量）的假设。由于表观遗传现象对遗传力估计的影响存在高度争议，因此研究结果将促进对这一重要问题的理解。因为研究人员可以发现DNA甲基化是对OA的遗传可塑性反应的一种机制，对这一机制的了解将显著改善并有可能改变生物如何应对全球变化的预测模型。

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.