COLLABORATIVE RESEARCH: URoL : Epigenetics 2: Predicting phenotypic and eco-evolutionary consequences of environmental-energetic-epigenetic linkages

合作研究：URoL：表观遗传学 2：预测环境-能量-表观遗传联系的表型和生态进化后果

• 批准号: 1921465
• 负责人: Hollie Putnam
• 金额: $ 72.03万
• 依托单位: University of Rhode Island
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2025-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1921465&HistoricalAwards=false
• 关键词: COLLABORATIVE; RESEARCH; URoL; Epigenetics; Predicting

Living organisms may acclimate to environmental changes through epigenetic modifications to DNA, which alter the way genetic instructions are interpreted without altering the DNA code itself. While these modifications to organismal phenotype or function can be reversible, some of them may be inherited by offspring, potentially producing multiple, heritable outcomes from a single genome and affecting ecological and evolutionary outcomes. This project uses symbiotic, metabolically complex reef building corals as a model system to test the connections between physiological, epigenetic, and metabolic states, and predict how population and community dynamics are influenced by epigenetically-modulated phenotypes. This work will advance biological knowledge by delineating fundamental links (Rules of Life) between ubiquitous organismal energetic processes, epigenetics, and eco-evolutionary outcomes. The Broader Impacts activities parallel the project's integrative approach, linking insights from Environment x Energetics x Epigenetics x Ecology for Education into an E5 platform. The E5 platform will provide i) early career STEM training, ii) local and global community education, and iii) educational resources for open science, quantitative approaches, and research reproducibility. Further, this E5 platform will train and inform the next generation of diverse scientists and public by combining local and global initiatives focusing on groups underrepresented in STEM. This project examines how nutrient metabolism in the mitochondria generates cofactors and energy that will instruct the epigenetic machinery in the cell nucleus to modulate genome function to appropriately respond to environmental conditions. Environmentally-responsive metabolic function and energetic-epigenetic linkages act as drivers of complex emergent phenotypes. To elucidate relationships that are the basis for Rules of Life with respect to epigenetics, this project will use integrative experimental and modeling approaches focused on reef building corals to: 1) link nutritionally-provisioned metabolites with epigenetic and organismal state through seasonal sampling across environmental gradients; 2) expand current Dynamic Energy Budget (DEB) models for symbiotic organisms to further integrate critical facets of nutritional symbiosis and calcification; 3) experimentally modulate metabolic and therefore epigenetic states through repeated exposure to increased temperature and nutrients, to test intra- and trans-generational epigenetic inheritance; 4) use DEB theory to identify shifts in energetics associated with epigenetic modulation, and link these sub-organismal processes to higher levels of organization; and 5) integrate findings into a generalizable, predictive eco-evolutionary model that links nutritional interactions, metabolic states, and subsequent epigenetic effects to the timescales regulating organismal processes and eco-evolutionary outcomes. This effort will provide characterization of environmental epigenetic phenomena in ecosystem-engineering marine invertebrates. This characterization includes determining the mechanisms and the degree of epigenetic 'memory' both within and across generations. By including information on environmental legacies, propagated by epigenetics, this project will advance both organismal and population-based models and improve capacity to predict responses to acute and chronic environmental signals.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

生物体可以通过 DNA 的表观遗传修饰来适应环境变化，这会改变遗传指令的解释方式，但不会改变 DNA 密码本身。虽然这些对生物体表型或功能的修饰是可逆的，但其中一些可能会被后代遗传，可能从单个基因组产生多种可遗传的结果，并影响生态和进化结果。该项目使用共生、代谢复杂的造礁珊瑚作为模型系统，测试生理、表观遗传和代谢状态之间的联系，并预测表观遗传调节表型如何影响种群和群落动态。这项工作将通过描绘普遍存在的有机体能量过程、表观遗传学和生态进化结果之间的基本联系（生命规则）来推进生物学知识。更广泛的影响活动与该项目的综合方法并行，将环境 x 能量学 x 表观遗传学 x 教育生态学的见解连接到 E5 平台。 E5 平台将提供 i) 早期职业 STEM 培训，ii) 本地和全球社区教育，以及 iii) 开放科学、定量方法和研究可重复性的教育资源。此外，这个 E5 平台将结合本地和全球针对 STEM 中代表性不足群体的举措，对下一代多元化科学家和公众进行培训和宣传。 该项目研究线粒体中的营养代谢如何产生辅助因子和能量，这些辅助因子和能量将指导细胞核中的表观遗传机制调节基因组功能，以适当地响应环境条件。环境响应代谢功能和能量表观遗传联系是复杂的新兴表型的驱动因素。为了阐明表观遗传学方面生命规则基础的关系，该项目将使用针对造礁珊瑚的综合实验和建模方法：1）通过跨环境梯度的季节性采样将营养供应的代谢物与表观遗传和生物体状态联系起来; 2）扩展当前的共生生物动态能量预算（DEB）模型，以进一步整合营养共生和钙化的关键方面； 3）通过反复暴露于升高的温度和营养物质来实验性地调节代谢以及表观遗传状态，以测试代内和跨代表观遗传； 4）使用DEB理论来识别与表观遗传调节相关的能量变化，并将这些亚有机过程与更高层次的组织联系起来； 5）将研究结果整合到一个可推广的、预测性的生态进化模型中，该模型将营养相互作用、代谢状态和随后的表观遗传效应与调节有机过程和生态进化结果的时间尺度联系起来。这项工作将提供生态系统工程海洋无脊椎动物中环境表观遗传现象的表征。这种表征包括确定代内和跨代的表观遗传“记忆”的机制和程度。通过纳入表观遗传学传播的环境遗产信息，该项目将推进有机体和基于群体的模型，并提高预测对急性和慢性环境信号的反应的能力。该奖项反映了 NSF 的法定使命，并通过评估被认为值得支持利用基金会的智力优势和更广泛的影响审查标准。

项目成果

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.

Reconciling the variability in the biological response of marine invertebrates to climate change

• DOI: 10.1242/jeb.245834
• 发表时间: 2023-09-01
• 期刊: JOURNAL OF EXPERIMENTAL BIOLOGY
• 影响因子: 2.8
• 作者: Dellaert，Zoe;Putnam，Hollie M.
• 通讯作者: Putnam，Hollie M.

Chronic low-level nutrient enrichment benefits coral thermal performance in a fore reef habitat

• DOI: 10.1007/s00338-021-02138-2
• 发表时间: 2021-06-29
• 期刊: CORAL REEFS
• 影响因子: 3.5
• 作者: Becker, Danielle M.;Putnam, Hollie M.;Silbiger, Nyssa J.
• 通讯作者: Silbiger, Nyssa J.