Tackling the methylome: recent methodological advances in genome-wide methylation profiling

In mammals, DNA methylation is predominantly, if not exclusively, found in CpG dinucleotides, due to site specificity of the known DNA methyltransferases [1]. Although it was reported in the early 1960s that cytosines can be methylated, it was not until two decades later that DNA methylation was fully recognized as an important player in gene regulation [2-4]. By acting coordinately with histone tail modifications and recruitment of an array of proteins involved in chromatin condensation, DNA methylation participates in gene silencing, independently of changes in DNA sequence [5]. The large majority of CpG dinucleotides in the human genome are methylated, and this results in a depletion of CpG sites due to conversion to thymines by deamination [6,7]. Unmethylated CpG sites escape depletion and are clustered in relatively small areas called CpG islands. A widely accepted definition of CpG islands was formulated by Gardiner-Garner and Frommer and takes into account local GC content, observed-to-expected frequency of CpGs and length of the region [8]. The exact meaning of these parameters has been disputed in recent publications and alternative definitions have been proposed in an attempt to better match definition of CpG islands to biological function [9-11]. Regardless of the definition, roughly one-third of CpG islands overlap with gene promoters, and as many as 70% of human promoters are associated with a CpG island. The vast majority of these promoter-associated CpG islands are unmethylated in normal tissues in both active and inactive genes, thus do not explain tissue-specific gene expression [12]. Exceptions to this general pattern are imprinted genes, X-inactivated genes in women, and germ-cell-restricted genes where promoter CpG island methylation is present [13]. Outside of CpG islands, the bulk of methylated cytosines in normal tissues is found in repetitive DNA elements, mostly retrotransposons of LINE and SINE classes [14].DNA methylation is an extremely d