Changes in hereditary information not only provide the basis of morphological diversity during evolution, but also pertain to a number of important contemporary issues such as crop improvement and the diagnosis or treatment of many human diseases. A great deal of effort has been dedicated to characterize the link between genetic mutations (i.e. DNA sequence or structural changes) and traits. In addition, the recent discovery of epigenetic mutations (epimutations), as defined by heritable changes in gene expression in the absence to any changes in the DNA sequence, have unveiled the importance of gene silencing pathways in development. Epimutations often differ from each other based on a chemical modification to their DNA, referred to as DNA methylation. Several pathways responsible for the establishment, maintenance and removal of DNA methylation have been characterized. However, very little is known about the origin, stability and the functional consequences of spontaneous epimutations, which occur naturally in nature. Part of my postdoctoral research was focused on using technologies that can identify the methylation status of each cytosine, one of the four main components of DNA, in a genome to characterize the frequencies of spontaneous epimutations in the model plant species, Arabidopsis thaliana. Our current research aims to understand how epimutations form in individuals, how they are maintained through cell divisions and how they are maintained over generational timescales. Our long-term goals are to learn about mechanisms that control establishment and maintenance of DNA methylation such that we can engineer these pathways to specifically control gene expression. It is expected that results from this research will not only help in our general understanding of how organisms program and maintain proper expression of genes, but will also lead to approaches that improve the stability, yield, and nutritional value of a variety of crops.