Genome-wide high-resolution mapping
and functional analysis of
DNA methylation in Arabidopsis

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes although the extent to which this DNA modification functions to regulate the genome is still unknown. Using a tiling microarray with 35 bp resolution, we carried out the first comprehensive mapping of DNA methylation in the entire genome of the flowering plant Arabidopsis thaliana. Pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs were heavily methylated. Unexpectedly, over one third of expressed genes contained methylation within transcribed regions, whereas only ~5% of genes contained methylation within promoter regions. Interestingly, genes methylated in transcribed regions were highly expressed and constitutively active, whereas promoter-methylated genes showed a greater degree of tissue-specific expression. Whole-genome tiling array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic non-coding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.