Understanding the mechanistic origins and evolution of gene body DNA methylation

DNA甲基化是真核生物基因组的一个基本特征。DNA甲基化的主要研究作用与其在基因表达失活中的作用有关。然而，DNA甲基化也在表达基因的子集中发现，这种DNA甲基化是如何在这些基因上产生的，其确切功能尚不清楚。奇怪的是，在这些表达的基因中存在基因体DNA甲基化，这表明DNA甲基化可能在不受基因调控的情况下发挥新的作用。该项目将支持本科生、研究生和博士后研究人员在实验生物学和计算生物学方面的培训。这些研究生还将参与指导由佐治亚大学赞助的Young Dawgs项目的高中暑期实习生。该奖项还将资助佐治亚大学遗传学系研究生开设的研究交流和专业发展研究生课程。多位在学术界之外从事科学事业的外部演讲者将被邀请到这门课上介绍他们的职业道路，并花一整天的时间与研究生互动。这个项目的目标是用植物作为模型系统来理解基因体DNA甲基化起源的分子基础。我们发现，在真核生物中，基因体DNA甲基化已经丢失。基因体DNA甲基化的缺失伴随着染色体甲基转移酶3(CMT3)的缺失，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了独立的验证，表明CMT3对于基因体DNA甲基化的起源和维持是重要的。我们以前的工作表明，拟南芥CMT3的表达导致了一组基因的异位甲基化，这让我们假设，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。在这个提案中，我们将探索组蛋白修饰H3K9me2和小RNA在建立基因体DNA甲基化中的作用。我们还将研究H3K9去甲基酶在检测全基因组水平的异染色质和塑造基因体DNA甲基化模式中的进化保守性和作用。这些问题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优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.