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Abstract
DNA methylation is a key chromatin modification and has been found in all studied plants. Currently, whole-genome bisulfite sequencing (WGBS) is the gold-standard method to detect DNA methylation at single-base resolution. This modification is associated with the silencing of transposable elements (TE) and certain genes. Some genes controlling agriculturally important traits are silenced by DNA methylation in the plant genomes. In addition, the role of DNA methylation has not been explicitly explored in many biological processes associated with the quality of agriculturally significant crops. My dissertation consists of three projects that focused on different aspects of DNA methylation in plants. In the first project, I determined that reads derived from methylated DNA are over-represented in WGBS. This finding paves the foundation to further increase the accuracy of estimating methylation levels. In the second project, I developed a novel method, termed epimutagenesis, to rapidly generate variation in DNA methylation through heterologous expression of a human ten-eleven translocation (TET) enzyme, which I show can randomly demethylate a plant genome. The use of TET-mediated engineering of DNA methylation states in economically and agriculturally significant plant species will be an interesting area of future investigation. In the third project, I completed a comprehensive genome-wide investigation of the epigenome during somatic embryogenesis in soybean. I identified a built-in process for reinforcing the regions possessing pre-existing non-CG methylation to maintain genome integrity during somatic embryogenesis over the short term, which eventually decays over longer time scales. The uncovered epigenomic instability resulting from continuous rounds of cell division reveals one source for epiallele formation in species possessing DNA methylation.