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一个子集中被发现，这种DNA甲基化是如何在这些基因上产生的，它的确切功能是未知的。令人好奇的是，基因体DNA甲基化存在于这些表达的基因中，这表明DNA甲基化可能独立于基因调控之外发挥新的作用。该项目将支持培养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。研究生们还将参与指导佐治亚大学赞助的“年轻的狗”项目的高中暑期实习生。该奖项还将支持乔治亚大学遗传学系研究生的研究交流和专业发展研究生课程。多位在学术界以外从事科学事业的外部演讲者将被邀请到这门课上，展示他们的职业道路，并花一整天的时间与研究生互动。该项目的目的是了解基因体DNA甲基化起源的分子基础，以植物为模型系统。我们发现，在salsugineum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质甲基化酶3 （CMT3）的缺失，这是一种维持异染色质相关DNA甲基化的DNA甲基化转移酶。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对基因体DNA甲基化的起源和维持很重要。我们之前的工作表明拟南芥CMT3的表达导致基因亚群的异位甲基化，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起作用。在本提案中，我们将探讨组蛋白修饰H3K9me2和小rna在建立基因体DNA甲基化中的作用。我们还将研究进化保护和H3K9去甲基化酶在全基因组异染色质水平检测和塑造基因体DNA甲基化模式中的作用。这些问题将有助于我们确定基因体DNA甲基化的机制起源，以及真核生物中DNA甲基化的潜在表达无关功能。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值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.