DNA methylation patterns in different genomic regions. Methylation patterns were characterized in following functional regions: TEs, small RNA (smRNA) loci, and genic regions including the promoter (200 bp upstream of the transcriptional start site, TSS), gene body (the entire transcribed region), and the transcriptional termination region (TTR, 200 bp downstream of transcriptional termination site). Gene body is further divided into untranslated regions (UTRs), coding regions (CDs), and introns. Methylation level, TE density and smRNA locus density were calculated across TE, gene body and their flanking sequences using an overlapping sliding window of 5% of the sequence length at a step of 2.5% of the sequence length. (a) Fraction of total mCs in each sequence context for different genomic regions. (b) Relative methylation level (total methylation level of mCs divided by sequence length of the calculated region) in each sequence context for different genomic regions. Distributions of absolute methylation level (total methylation level of mCs divided by total number of cytosine sites in the calculated region) (c) and relative methylation level (d) in gene body and 2-kb flanking sequences on both sides. Absolute (e) and relative (f) methylation level distributions in TE and 0.5-kb flanking sequences on both sides. (g) TE and smRNA density distributions in gene body and 2-kb flanking sequences. (h) smRNA density distribution throughout TE and 0.5 kb-flanking sequences. Relationships between methylation level and sequence length in genes (i) and TE regions (j), in which both absolute (top) and relative (bottom) methylation levels were analyzed.