Investigating the mechanistic origins, maintenance and functions of gene body DNA methylation in plants

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In the genomes of most eukaryotes, methylation of cytosine bases in DNA is a common modification that has long been believed to down-regulate, or turn off, gene expression. This view has been challenged by recent studies showing that the effect on gene expression depends on where the methylation occurs. In many organisms including humans and some plants, DNA methylation located next to a gene turns the gene off, whereas DNA methylation located within the gene-body is found in genes that are active. This project seeks to understand why this pattern is true. Using plants as study organisms, genetic tools have been used to introduce gene-body methylation into the genome of a plant that normally lacks this type of methylation. This experimental manipulation simulates the evolutionary origin of gene-body methylation. Therefore, by studying the resulting effects on gene expression and fitness traits over multiple generations, this project will provide new insights about the origins and function of this intriguing pattern of DNA methylation. The project will also support several educational activities. The research will be carried out by a postdoctoral fellow and a graduate student, who will be trained in experimental and computational biology. Open-source software and instructional materials will be developed for teaching introductory principles of genetics via computer-simulated problem-solving, as a complement to traditional lectures. High school students will be mentored during summer internships sponsored by the University of Georgia Young Dawgs Program. Cytosine DNA methylation in the promoters of genes is typically associated with transcriptional repression. By contrast, gene-body methylation (gbM) is often found on actively transcribed genes. This relationship of DNA methylation to gene expression suggests that gbM has distinct functions. In mammals some of these functions are known, whereas in plants and insects, these functions appear to be distinct, though as yet poorly characterized. In no case are the mechanisms that establish DNA methylation in gene bodies understood. To gain insight into the origin and specificity of gbM, this project will use two related plant species as models: Arabidopsis thaliana (in which gbM is catalyzed by the CMT3 methyltransferase) and Eutrema salsigineum (which lacks CMT3 and gbM). In preliminary studies, introduction of the Arabidopsis CMT3 gene into Eutrema leads to gbM. To follow this observation, experiments will test several hypotheses to understand the molecular basis for gbM, what genes acquire gbM, how those genes are targeted, and what role may be played by a newly identified chromosomal histone modification (H3K23 methylation). The outcomes have the potential to reveal important undiscovered functions of DNA methylation in regulating chromatin-mediated gene expression in higher 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.