Understanding the mechanistic origins and evolution of gene body DNA methylation

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.