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 different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. We have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single nucleotide resolution maps of DNA methylation. We find that DNA methylation is site-specifically regulated by different factors. Furthermore, we have identified novel regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning.