Understanding the mechanistic origins and evolution of gene body DNA methylation

了解基因体 DNA 甲基化的机制起源和进化

• 批准号: 2242696
• 负责人: Robert Schmitz
• 金额: $ 88万
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2242696&HistoricalAwards=false
• 关键词: Understanding; mechanistic; origins; evolution; gene

DNA methylation is a fundamental feature of eukaryotic genomes. The primary studied role of DNA methylation relates to its role in inactivating gene expression. However, DNA methylation is also found in the bodies of a subset of expressed genes and how this DNA methylation originates at these genes and its exact function is unknown. It is curious that gene body DNA methylation exists in these expressed genes, which points to possible new roles for DNA methylation independent of gene regulation. This project will support training of undergraduate, graduate and postdoctoral researchers in both experimental and computational biology. The graduate students will also participate in mentoring high-school summer intern students from the Young Dawgs program sponsored by the University of Georgia. This award will also support a graduate course in research communications and professional development taken by graduate students in the Department of Genetics at the University of Georgia. Multiple outside speakers that have pursued scientific careers outside of academia will be invited to this class to present their career path and spend the entire day interacting with graduate students. The goal of this project is to understand the molecular basis for the origins of gene body DNA methylation using plants as model systems. We discovered that gene body DNA methylation has been lost in Eutrema salsugineum. The loss of gene body DNA methylation was accompanied by the loss of CHROMOMETHYLASE 3 (CMT3), a DNA methyltransferase that maintains heterochromatin associated DNA methylation. This discovery was independently validated in multiple independent plant species suggesting that CMT3 is important to the origins and maintenance of gene body DNA methylation. Our previous work showed the expression of Arabidopsis thaliana CMT3 led to ectopic methylation at a subset of genes leading us to hypothesize that machinery required for maintenance of heterochromatin also functions in gene bodies in euchromatin. In this proposal, we will explore the role of the histone modification H3K9me2 and small RNAs in the establishment of gene body DNA methylation. We will also investigate the evolutionary conservation and the role of an H3K9 demethylase in sensing genome-wide levels of heterochromatin and shaping gene body DNA methylation patterns. These lines of query will help us establish the mechanistic origins of gene body DNA methylation, and potential expression-independent functions of DNA methylation in eukaryotes.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.

DNA甲基化是真核生物基因组的基本特征。DNA甲基化的主要研究作用涉及其在失活基因表达中的作用。然而，DNA甲基化也存在于一部分表达基因的体内，这种DNA甲基化如何起源于这些基因及其确切功能尚不清楚。令人好奇的是，基因体DNA甲基化存在于这些表达基因中，这指出了DNA甲基化可能独立于基因调控的新作用。该项目将支持实验生物学和计算生物学的本科生、研究生和博士后研究人员的培训。研究生还将参加由格鲁吉亚大学赞助的“年轻的道格”项目的高中暑期实习生辅导。该奖项还将支持研究生在遗传学系在格鲁吉亚大学采取的研究通信和专业发展的研究生课程。多位在学术界以外从事科学事业的外部演讲者将被邀请参加这门课程，介绍他们的职业道路，并花一整天的时间与研究生互动。该项目的目标是以植物为模型系统，了解基因体DNA甲基化起源的分子基础。我们发现盐地菜基因体DNA甲基化已经丢失。基因体DNA甲基化的丧失伴随着染色体甲基化酶3（CMT3）的丧失，CMT3是一种维持异染色质相关DNA甲基化的DNA甲基转移酶。这一发现在多个独立的植物物种中得到独立验证，表明CMT3对基因体DNA甲基化的起源和维持很重要。我们以前的工作表明，拟南芥CMT3的表达导致了一个基因子集的异位甲基化，这使我们假设，维持异染色质所需的机制也在常染色质的基因体中发挥作用。在本研究中，我们将探讨组蛋白修饰H3K9me2和小RNA在基因体DNA甲基化建立中的作用。我们还将研究H3K9去甲基化酶在感知全基因组异染色质水平和塑造基因体DNA甲基化模式中的进化保守性和作用。这些疑问将帮助我们建立基因体DNA甲基化的机制起源，以及真核生物中DNA甲基化的潜在表达独立功能。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值进行评估而被认为值得支持。和更广泛的影响审查标准。

项目成果

An evolutionary epigenetic clock in plants

• DOI: 10.1126/science.adh9443
• 发表时间: 2023-09-29
• 期刊: SCIENCE
• 影响因子: 56.9
• 作者: Yao，N.;Zhang，Z.;Johannes，F.
• 通讯作者: Johannes，F.