Epigenomic Consequences of Increased Heterochromatin Load in Maize

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。Jered M. Wendte博士的研究和培训计划的标题是“玉米异染色质负荷增加的表观基因组后果”。该奖学金的主办机构是佐治亚大学，赞助科学家是罗伯特·j·施米茨博士。人类面临的一个主要问题是为成倍增长的人口生产足够的食物供应。解决这一问题的一个有希望的策略是通过基因组工程对作物基因组进行修改，以产生具有更高产量和理想性状的作物品种。植物基因组由几段长长的DNA组成，称为染色体。每条染色体编码数千个基因，这些基因提供了生物体的蓝图。本项目将通过评估两种潜在的基因组工程策略，推进玉米这一重要谷类作物的基因组工程技术。第一种方法是向玉米中添加全新的染色体，以引入由多个基因编码的理想性状。第二种方法是将编码蛋白质的基因添加到玉米中，这些蛋白质可以化学修饰DNA，作为增加玉米性状多样性的一种手段，然后可以选择玉米的理想性状，例如抗旱或抗病。培训目标包括基因组学、生物信息学和科学传播。更广泛的影响包括参与旨在向西班牙裔和美洲原住民社区介绍植物基因组学机会的现有项目。染色质的表观遗传修饰通过靶向重复序列，如转座因子（te），在异染色质形成和转录沉默中起着维持基因组稳定性的关键作用。在植物中，相对较大的基因组主要由针对异染色质形成的te组成，因此异染色质在表型多样性中也起着重要作用。在植物物种之间，异染色质修饰的数量和分布在基因组中存在显著差异。此外，在物种内，染色质状态或外显子的遗传变化是表型变异的重要来源。然而，目前缺乏对这些现象的机制解释，包括影响总体异染色质容量变化的因素和导致外等位基因形成的启动事件。利用先进的基因组学技术和新的玉米遗传资源，该项目将解决这些知识空白：1)确定细胞是否？通过评估以多余B染色体的形式引入大量、多碱基数量的遗传物质对玉米异染色质结构的影响，哪些因素可能是限制性的；2)通过鉴定玉米DNA甲基转移酶的异源表达，确定甲基转移酶的靶向决定因素及其在表观等位基因形成启动事件中的作用。所有数据将通过公共存储库提供，包括NCBI （https://www.ncbi.nlm.nih.gov/）和主办实验室网站（http://schmitzlab.genetics.uga.edu/data）。如果成功，该项目将提供新的重要信息，可用于帮助指导作物基因组工程设计策略，使人工染色体对异染色质调控途径的有害影响最小。项目结果还将有助于评估表观基因组调节策略的潜力，以诱导表型变异，从而选择理想性状。关键词：玉米，表观遗传学，DNA甲基化，异染色质，人工染色体，基因组工程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. Jered M. Wendte is "The Epigenomic Consequences of Increased Heterochromatin Load in Maize". The host institution for the fellowship is the University of Georgia and the sponsoring scientist is Dr. Robert J. Schmitz.A major problem facing humanity is the production of an adequate food supply for an exponentially increasing population. One promising strategy to address this problem is the modification of crop plant genomes to produce crop varieties with higher yields and desirable traits through genome engineering. Plant genomes are comprised of several long stretches of DNA, termed chromosomes. Each chromosome encodes thousands of genes, which provide the blueprint of an organism. This project will advance genome engineering technologies in the important cereal crop, maize, by evaluating two potential genome engineering strategies. The first involves the possibility of adding entirely new chromosomes to maize as a means to introduce desirable traits that are encoded by multiple genes. The second involves adding genes that encode proteins that chemically modify DNA to maize as a means to increase trait diversity in maize, which can then be selected on for desirable traits, such as drought or disease resistance. Training objectives include genomics, bioinformatics, and science communication. Broader impacts include participation in existing programs directed at introducing Hispanic and Native American communities to opportunities in plant genomics sciences. Epigenetic modification of chromatin plays a critical role in the maintenance of genomic stability by targeting repetitive sequences, such as transposable elements (TEs), for heterochromatin formation and transcriptional silencing. In plants, which are characterized by relatively large genomes mostly comprised of TEs that are targeted for heterochromatin formation, heterochromatin also plays an important role in phenotypic diversity. Between plant species, there is remarkable variation in the amount and distribution heterochromatin modifications within genomes. Also, within species, heritable changes in chromatin state, or epialleles, account for an important source of phenotypic variability. However, mechanistic explanations for these phenomena, including factors that influence variation in overall heterochromatin capacity and the initiating events that lead to epiallele formation, are currently lacking. Using advanced genomics techniques and novel genetic resources in maize, this project will address these knowledge gaps by 1) determining if a cell?s capacity for heterochromatin is limited, and what factors could be rate limiting by assessing the impacts of the introduction of large, multi-megabase quantities of genetic material in the form of supernumerary B chromosomes on maize heterochromatin structure; and 2) identifying the determinates of methyltransferase targeting and their role in the initiating events of epiallele formation by assessing the heterologous expression of DNA methyltransferases in maize. All data will be made available through public repositories including NCBI (https://www.ncbi.nlm.nih.gov/) and the host laboratory website (http://schmitzlab.genetics.uga.edu/data). If successful, this project will provide new important information that can be applied to help guide crop genome engineering design strategies for artificial chromosomes that have minimal detrimental impacts on heterochromatin regulatory pathways. Project outcomes will also help assess the potential of strategies for modulation of the epigenome to induce phenotypic variability that can be selected on for desirable traits.Keywords: maize, epigenetics, DNA methylation, heterochromatin, artificial chromosomes, genome engineeringThis 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.