DNA Methylation Profiling from High-Throughput Sequencing Data

The methylation of a cytosine at the carbon 5 position (5meC) is a common epigenetic mark in eukaryotic cells that is normally found in CpG and CpHpG (H=A,C,T) sequence contexts. The inactivation of one of the X-chromosomes in female cells, the allele-specific expression of imprinted genes or the role in the embryonic development which is shown by the early lethality of Dnmt3a and Dnmt3b deficient mice are only some of the important functions that DNA methylation plays (Chen and Li, 2004; Dodge, et al., 2005; Karpf and Matsui, 2005; Okano, et al., 1999). The methylation of the gene promoter region is commonly associated with silenced transcription; however recently it was shown that the DNA methylation in the gene body of transcribed genes is increased in both animals and plants (Hellman and Chess, 2007; Jones, 1999; Zhang, et al., 2006). Furthermore, CHG methylation relates to the silencing of transposons in plants (Miura, et al., 2009) . Given all these facts, it is clear that the DNA methylation pattern along the genome sequence carries valuable biological information and is crucial for our understanding on gene expression and developmental control. Furthermore, it can reveal how aberrant epigenetic changes might lead to dysregulation of gene expression and to the development of diseases such as cancer (Costello, et al., 2000).