Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.

Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in a sequence specific manner. What factors regulate DNA methylation at a given site in the genome largely remains elusive. Here by generating single nucleotide resolution maps of DNA methylation we have surveyed the effect of mutations in a comprehensive list of genes involved in gene silencing in Arabidopsis. We find that DNA methylation is site-specifically regulated by different factors. Furthermore, we have identified novel regulators of DNA methylation. We have generated a comprehensive resource to further understanding the control of DNA methylation patterning. Whole genome methylation maps of 86 silencing mutants involved in gene silencing and chromatin modifications were generated using BS-seq (Cokus et al., Nature 2008 ). Wild type replicate 1 dataset can be found at GSM938370.