Methylome Variation Within and Between Isogenic Arabidopsis thaliana Individuals

Heritable epigenetic marks, such as cytosine methylation, can be sources of phenotypic variation. In order to understand their role in evolution, it is important to ascertain the intrinsic variability and stability of such marks. Previous studies in Arabidopsis thaliana have described and quantified the stability and emergence of DNA methylation variability across multiple generations. The degree of epigenetic variation within an individual plant as well as between individuals from the same generation has, however, remained elusive. 

We have compared the methylomes of (i) different organ types and (ii) a series of leaves from the same individual as well as of the corresponding leaves from different individuals. Organ type had the greatest effect on methylome variation, while analogous leaves from different individuals were the most similar. Importantly, there appears to be an ordered progression among a series of consecutive leaves from the same plant. Since these were harvested at the same time point, these methylation polymorphisms reflect changes in leaf identity, rather than temporal progression of the entire plant. In conclusion, we have been able to identify unique patterns that change systematically with leaf development, and provide insights on the variability of epigenetic marks in short time scales.