Genome wide methylation profiling reveals methylation differences between reproductive and vegetative organ systems

DNA methylation is an epigenetic mark that is not only important for silencing of plant transposable elements, but that can also influence gene expression. Previous studies with Arabidopsis thaliana have addressed inter-individual variation and the effects of stresses on DNA methylation, while less is known about changes in DNA methylation associated with development. In this study we investigated intra- and inter-individual differentiation of the genome-wide methylome across six different organ types from three A. thaliana individuals, descended from a single founder plant. We find that DNA methylation varies significantly between organ types, with reproductive organs having substantial relative gains of DNA methylation compared to vegetative organs. Methylated regions upstream or downstream of genes can affect gene expression, but only when they overlap with a transposable element. Our work suggests that methylation changes systematically during plant development, and that these changes may reinforce the action of transcriptional regulators during development.