Natural Variation of Arabidopsis thaliana DNA Methylome

Taking advantage of next-generation sequencing technologies, we resequenced the genome, methylome and transcriptome of around 200 wild accessions of Arabidopsis thaliana collected in their natural habitat in Sweden and regrown under two controlled environments (10C and 16C). We explored the natural variation of previously described features of the Arabidopsis thaliana methylome, and how this impacted the variability of gene expression, integrating the additional knowledge of SNP variation in that population. Though methylation pattern are well conserved between ecotypes and environments,  differences in CHH methylation were detected between different temperature environments. By applying Genome Wide Association Mapping (GWAS), we identified trans-factors contributing to global CHH and CpG methylation. We were able to distinguish two types of DNA methylation differing by their structural properties, their combination of different types of methylation in either the CG, CHG or CHH context, and the variability of their local DNA methylation pattern across all the re-sequenced 280 methylomes. These structural differences also overlapped with fundamental functional differences in the way these different types of methylation associate with genes and transposable elements and with the regulation of their expression and silencing. Finally, we explored the natural variation and potential history of selection of these different types of methylation regions. We have shown DNA methylation patterns of natural Arabidopsis population are tightly controlled by the genotype, while DNA methylation affects the composition of the genome possibly by de-amination of methylated sites and different selection pressure on the nucleotide change.