Mechanisms of physiological plasticity in early stage marine invertebrates in response to multiple stressors - epigenomic perspective in a global change context

早期海洋无脊椎动物响应多种应激源的生理可塑性机制——全球变化背景下的表观基因组视角

基本信息

批准号：
1656262
负责人：
Gretchen Hofmann
金额：
$ 75.59万
依托单位：
University of California-Santa Barbara
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2017
资助国家：
美国
起止时间：
2017-03-15 至 2023-02-28
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1656262&HistoricalAwards=false
关键词：
Mechanisms physiological plasticity early stage

项目摘要

The ocean is often viewed as vast and immutable, capable of absorbing environmental change. However, we are increasingly aware that the ocean does things for us as humans (e.g. by providing seafood, and even the oxygen we breath that comes from the activity of billions of marine phytoplankton), and further, that these ocean services are threatened by changes in ocean chemistry because of increased carbon dioxide in the atmosphere. To expand our knowledge about the vulnerability of marine ecosystems, the goal of this project is to study the resilience of marine organisms to environmental change by examining the tolerance of their early stages (embryos and larvae) to stresses in the ocean such as higher temperatures and changes in ocean chemistry. The study organism of this project is the purple sea urchin, a common marine invertebrate found on the California coast. Although this might seem like an odd choice, purple urchins have been model study organisms in developmental biology and scientists know a great deal about their embryos' development. For the project, the researchers will use molecular biology tools, some that were developed in human cancer biology, to determine how the timing of gene expression can improve the success of embryos and larvae in the face of environmental stress. New insight from this project will likely shed some light, and some hope, on how, and how fast, marine organisms can adjust to changes in their marine environment. The goal of this project is to study the "genome to phenome" concept, and to investigate mechanisms that contribute to rapid shifts in organismal physiological capacities in response to environmental change, processes that would operate on ecological rather than evolutionary time scales. The model system is the early life-history stages of the purple sea urchin Strongylocentrotus purpuratus, and the PIs will focus on two processes: intragenerational plasticity and transgenerational plasticity (TGP) where they will specifically interrogate epigenetic mechanisms that may alter gene expression in early stage urchins on a rapid time scale. For the environment-organism interaction, the PIs will focus on co-occurring multiple abiotic factors (pCO2, oxygen and temperature) that are ecologically relevant, are highly variable in the purple urchin nearshore habitat, and are projected to change drastically in future climate change scenarios. The project will explore ecological epigenomics in a global change context. Methodologically, the PIs plan to do the following: (1) raise cultures of sea urchins at variable pCO2 and temperature conditions followed by assays to test physiological tolerances of the progeny (growth, metabolic rate and lipid content), (2) use two screening assays for global patterns of DNA methylation: an ELISA-based method that measures levels of 5-methylcytosine (5-mC) in samples of genomic DNA, and the methylation-sensitive amplification polymorphism (MSAP) assay, (4) use RNA-Seq to assess gene expression patterns, and (5) perform concurrent profiling of the larval transcriptome and methylome using Illumina® sequencing technology, in this case, RNA-Seq combined with whole genome bisulfite methylation sequencing.

海洋通常被认为是广阔且不可改变的，能够吸收环境变化。然而，我们越来越意识到海洋为我们人类做着很多事情（例如，通过提供海鲜，甚至提供我们呼吸的来自数十亿人活动的氧气。海洋浮游植物），此外，由于大气中二氧化碳的增加，这些海洋服务受到海洋化学变化的威胁。为了扩大我们对海洋生态系统脆弱性的了解，该项目的目标是研究海洋生态系统的恢复力。海洋生物对环境的影响通过检查其早期阶段（胚胎和幼虫）对海洋压力（例如高温和海洋化学变化）的耐受性，该项目的研究生物是紫海胆，这是一种在加利福尼亚海岸发现的常见海洋无脊椎动物。尽管这似乎是一个奇怪的选择，但紫海胆一直是发育生物学中的模型研究生物，科学家们对其胚胎的发育了解很多，在该项目中，研究人员将使用分子生物学工具，其中一些是在人类癌症中开发的。生物学，至确定基因表达的时机如何提高胚胎和幼虫在面对环境压力时的成功率，该项目的新见解可能会为海洋生物如何以及以多快的速度适应变化带来一些启示和希望。该项目的目标是研究“基因组到现象组”的概念，并研究导致生物体生理能力快速转变以响应环境变化的机制，该过程将在生态时间而不是进化时间上进行。模型系统是早期的。紫海胆 Strongylocentrotus purpuratus 的生命史阶段，PI 将重点关注两个过程：代内可塑性和跨代可塑性 (TGP)，他们将专门研究可能快速改变早期海胆基因表达的表观遗传机制对于环境-生物相互作用，PI 将重点关注同时发生的多种非生物因素（pCO2、氧气和温度），这些因素与生态相关、高度相关。紫海胆近岸栖息地的变化，预计会在未来的气候变化情景中发生根本性的变化。该项目将在全球变化背景下探索生态表观基因组学，PI 计划采取以下措施：（1）培养海胆。在可变的 pCO2 和温度条件下，然后进行测定来测试后代的生理耐受性（生长、代谢率和脂质含量），(2) 使用两种筛选测定法来检测 DNA 甲基化的整体模式：基于 ELISA 的测定法测量基因组 DNA 样本中 5-甲基胞嘧啶 (5-mC) 水平的方法，以及甲基化敏感扩增多态性 (MSAP) 测定，(4) 使用 RNA-Seq 评估基因表达模式，以及 (5) 并行执行使用 Illumina® 测序技术对幼虫转录组和甲基化组进行分析，在本例中，RNA-Seq 与全基因组亚硫酸氢盐甲基化测序相结合。

项目成果

期刊论文数量（12）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Exploring impacts of marine heatwaves: paternal heat exposure diminishes fertilization success in the purple sea urchin (Strongylocentrotus purpuratus)

探索海洋热浪的影响：父本受热会降低紫海胆 (Strongylocentrotus purpuratus) 的受精成功率

DOI：
10.1007/s00227-021-03915-x
发表时间：
2021
期刊：
Marine Biology
影响因子：
2.4
作者：
Leach, Terence S.;BuyanUrt, Buyanzaya;Hofmann, Gretchen E.
通讯作者：
Hofmann, Gretchen E.

Parental environments alter DNA methylation in offspring of the purple sea urchin, Strongylocentrotus purpuratus

亲本环境改变紫海胆（Strongylocentrotus purpuratus）后代的 DNA 甲基化

DOI：
10.1016/j.jembe.2019.03.002
发表时间：
2019
期刊：
Journal of Experimental Marine Biology and Ecology
影响因子：
2
作者：
Strader, M.E.;Wong, J.M.;Kozal, L.C.;Leach, T.S.;Hofmann, G.E.
通讯作者：
Hofmann, G.E.

Examining the Role of DNA Methylation in Transcriptomic Plasticity of Early Stage Sea Urchins: Developmental and Maternal Effects in a Kelp Forest Herbivore

检查 DNA 甲基化在早期海胆转录组可塑性中的作用：对海带森林食草动物的发育和母体影响

DOI：
10.3389/fmars.2020.00205
发表时间：
2020
期刊：
Frontiers in Marine Science
影响因子：
3.7
作者：
Strader, Marie E.;Kozal, Logan C.;Leach, Terence S.;Wong, Juliet M.;Chamorro, Jannine D.;Housh, Madeline J.;Hofmann, Gretchen E.
通讯作者：
Hofmann, Gretchen E.

The effects of temperature and pCO2 on the size, thermal tolerance and metabolic rate of the red sea urchin (Mesocentrotus franciscanus) during early development