(A) Microarray data from Chromosome 4 are displayed for a 125-kb region 9 Mb from the nuclear organizing region (Figure S1). Open reading frames from genes (yellow) and retrotransposons (green) are indicated, along with repeats predicted by RepBase and TandemRepeatFinder. Small RNA matches from massively parallel signature-sequencing (MPSS) data are indicated. Tiles that represent significant CNPs are highlighted in purple (CGH), while tiles that detect significant DNA methylation are highlighted in red for the two ecotypes (5 mC, Col and Ler). Examples of a gene CNP (a), a TE CNP (b), and a methylation polymorphism (c) are boxed.
(B) Significant methylation was detected by microarray analysis for two representative genes in Ler (At4g40980) and Col (At4g28850), respectively. This methylation was verified by digestion of genomic DNA by McrBC, followed by PCR amplification using primers specific for each gene (lower panels). Failure to amplify a product after digestion by McrBC indicates that the gene is methylated. Control primers from an unmethylated tile (ta25c11) and a methylated transposon (TA2) indicate complete digestion and amplification in each case.