First High Resolution Rat Methylome Figure 2. Methylation density in different genomic regions. Methylation density within promoter, gene body and repeats was calculated by dividing the peak summit count in that region by the area of that region. Further repeats were classified in different classes and average methylation level of each class was calculated and plotted. doi:10.1371/journal.pone.0031621.g002 (Figure 6C, D). Despite significant divergence with respect to tissue and species, we still observe that UTRs are generally not marked by methylation, unless the exon they are a part of, also contains protein coding region. This highlights the conserved nature of DNA methylation pattern in protein coding sequences across species and tissue fates. To prove this point further, we analyzed the methylation status of ‘‘introns’’ that are known to be retained in the transcript (intron retention). We downloaded the Figure 3. Genomic distribution of methylated and unmethylated CGI. CpG Island of each methylated and unmethylated Islands were classified in different bins on the basis of size. A – Number of methylated CpG Islands in a particular bin was calculated in different regions like intron, exon, promoter (5 kb upstream from the transcription start site) and rest was put in others category. The count was then normalized by the total number of CpG Island in that bin. B – Number of unmethylated CpG Island of bin was calculated in different regions like intron, exon, promoter (5 kb upstream from the transcription start site) and others, and the count was then normalized by the total number of CpG Islands in that bin. doi:10.1371/journal.pone.0031621.g003 PLoS ONE | www.plosone.org 4 February 2012 | Volume 7 | Issue 2 | e31621