Identifying Deeply Conserved Patterns of Epigenetic Modification and Imprinting during Seed Development

本行动资助NSF国家植物基因组计划2018年度生物学博士后研究奖学金。该奖学金支持奖学金获得者在主办实验室的研究和培训计划，该奖学金获得者还提出了扩大生物学参与的计划。Rebecca Povilus博士的研究和培训计划的标题是“在种子发育过程中识别深度保守的表观遗传修饰和印记模式”。该奖学金的主办机构是Whitehead生物医学研究所，赞助科学家是Mary Gehring博士。种子对人类很重要；种子构成了我们的大部分饮食，是我们赖以生存的生态系统的重要组成部分。了解影响种子发育的因素对于改善种子作物（如小麦、玉米、水稻和大豆）以及在将遗传多样性重新引入自交系作物品种时确保产生可行的后代是必要的。直到最近才有技术和系统来阐明表观遗传修饰（DNA碱基和相关DNA包装蛋白的化学变化）在植物繁殖过程中所起的作用。虽然表观遗传修饰已被证明对少数远亲植物物种的种子发育很重要，但表观遗传修饰的实际模式和效果在物种之间似乎存在很大差异。为了预测基于表观基因组的作物改良和植物育种技术的应用范围，必须确定所有开花植物的基本或特定谱系的表观遗传修饰模式。这个项目将为理解表观遗传过程在开花植物繁殖过程中如何发挥作用提供一个缺乏的基础。为了做到这一点，表观遗传修饰及其与种子发育过程中基因表达的关联将在新兴的模式系统Nymphaea thermarum中进行鉴定，该系统是最古老的开花植物谱系之一。培训目标包括基因组学、表观基因组学和生物信息学。更广泛的影响包括通过怀特黑德合作伙伴计划与当地学校教师进行接触，并开发和分发早期科学教育模块，探讨生物多样性和基础研究对农业和粮食安全的重要性。该模块将作为阿诺德植物园夏季研究所的一部分，并将在https://nthermarum.weebly.com/.The上提供，该项目的目标是了解表观遗传修饰及其对种子发育过程中基因表达的影响。具体目标包括：1)通过甲基化DNA和组蛋白标记的免疫定位、甲基化敏感DNA测序和染色质谱分析，确定热玉米生殖发育过程中表观遗传修饰的动态；2)利用杂交和组织特异性基因表达分析，鉴定早期胚胎和胚乳发育过程中母系或父系印迹的基因。通过比较来自若虫的结果和来自模式物种的信息，深度保守的表观遗传修饰和印迹基因表达模式将与那些来自单子房（如谷类作物）或双子房（如拟南芥）的模式区分开来。该项目的结果将发表在开放获取的预印本服务器和同行评议的期刊上，信息将在网站https://nthermarum.weebly.com/.Keywords上提供：种子发育，胚胎，胚乳，表观遗传学，Nymphaea，比较基因组学和表观基因组学。该奖项反映了美国国家科学基金会的法定使命，并通过基金会的智力价值和更广泛的影响审查标准进行评估，认为值得支持。

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2018. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Dr. Rebecca Povilus is "Identifying Deeply Conserved Patterns of Epigenetic Modification and Imprinting during Seed Development". The host institution for the fellowship is the Whitehead Institute for Biomedical Research and the sponsoring scientist is Dr. Mary Gehring.Seeds are important for humans; seeds make up most of our diets and are a key part of the ecosystems that we depend on. Understanding what factors influence seed development is necessary to improve seed crops (such as wheat, corn, rice, and soybean), as well as to ensure the production of viable offspring when re-introducing genetic diversity into inbred crop varieties. Only recently have technologies and systems been available to elucidate the role that epigenetic modifications (chemical changes to DNA bases and to associated DNA-packaging proteins) play during plant reproduction. While epigenetic modifications have been shown to be important for seed development in a small number of distantly related plant species, the actual patterns and effects of epigenetic modification appear to vary substantially between species. To predict how broadly epigenome-based technologies for crop improvement and plant breeding can be applied, the patterns of epigenetic modifications that are fundamental to all flowering plants, or are specific to particular lineages must be determined. This project will provide an otherwise lacking foundation for understanding how the role that epigenetic processes play during reproduction has evolved across flowering plants. To do so, epigenetic modifications and their association with gene expression during seed development will be identified in the emerging model system Nymphaea thermarum, a member of one of the most ancient flowering plant lineages. Training objectives include genomics, epigenomics and bioinformatics. Broader impacts include outreach to local school teachers through the Whitehead Partner program and the development and distribution of a module for early-science education that explores the importance of biodiversity and basic research to agriculture and food security. This module will be presented as part of the Arnold Arboretum Summer Institute, and will be available at https://nthermarum.weebly.com/.The goal of this project is to understand epigenetic modification and its impact on gene expression during seed development. Specific objectives include 1) determining the dynamics of epigenetic modification during reproductive development in N. thermarum through immunolocalization of methylated DNA and histone marks, methylation-sensitive DNA sequencing and chromatin profiling and 2) identifying genes that are maternally- or paternally-imprinted during early embryo and endosperm development using hybrid crosses and tissue specific gene expression analysis. By comparing results from Nymphaea to information from model species, deeply conserved patterns of epigenetic modifications and imprinted gene expression will be distinguished from those that are derived within either monocots (such cereal crops) or eudicots (such as Arabidopsis). Results of this project will be published on open-access pre-print servers and peer-reviewed journals, and information will be available on the website https://nthermarum.weebly.com/.Keywords: seed development, embryo, endosperm, epigenetics, Nymphaea, comparative genomics and epigenomicsThis 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.