First High Resolution Rat Methylome Figure 7. Methylation marks the coding region. Third exon of the Ccdc 75 gene shows methylation in MeDIP-Seq data as visualized in UCSC genome browser. doi:10.1371/journal.pone.0031621.g007 available. Since of complex disorders have a metabolic component and liver is a key regulator of mammalian metabolism, we preferentially choose to look at the liver methylome. To our knowledge this is the first high resolution mammalian liver methylome and it is expected that the rat methylome generated in this study will help the research community to investigate aberrant DNA methylation in several complex disorders for which well established rat models already exist. Although MeDIP-Seq has several advantages, it runs a risk of generating false positive results especially when raw tags are directly used for assessing methylation levels. We used MACS to sharpen methylation peak summits for better score and thus overcome this problem, MACS improves the spatial resolution of aligned data and imparts robustness to the final alignment of sequences on the basis of a dynamic poisson distribution which corrects for local biases in the genome [23]. Since, this is the first report of rat methylome, we have several interesting observations. We observed that repeat regions in general are highly methylated. Approximately 41.9% of rat genome is covered by repeats which include ten different classes. Figure 8. Methylation in alternate splice events. Methylation in genomic features along with Intron retention class of alternative splicing events was calculated. Genomic features include RefSeq exons, introns, identified liver expressed gene exons and introns. Three bins were created: 1) 200 bp upstream from start site of the event, 2) from start site to end of the event, 3) 200 bp downstream from the end. Peak summit count obtained in all bins was normalized by dividing the count with the area of that bin. Distribution of peak summit count in 10 bp sliding window, 200 bp upstream and downstream from the start site of all RefSeq exons and cassette exons. doi:10.1371/journal.pone.0031621.g008 PLoS ONE | www.plosone.org 7 February 2012 | Volume 7 | Issue 2 | e31621