Figure 1.
Distribution of DNA methylation levels and the corresponding sequence context. (A) The percentage of methylated Cs was determined by taking the ratio of the number of methylated Cs over the total number of covered Cs. Methylation levels were grouped into five categories: unmethylated (U), intermediate between unmethylated and partially methylated (U_P), partially methylated (P), intermediate between partially methylated and methylated (M_P), and methylated (M). Levels of methylation were found to be highest in undifferentiated hESCs at ∼6% with a reduction in the differentiated cells. The fully differentiated peripheral blood mononuclear cells (monocytes) had the lowest methylation levels at ∼3%. Note: the monocyte data were provided as a base-level methylome map for comparison purposes only (Jun Wang, Beijing Genome Institute). (B) DNA methylation in various combinations of sequence contexts (CH, HC, CHH; H = any four nucleotides) throughout the genome was examined. In the CH sequence context, CpG methylation was the predominant form, but a significant fraction of methylated cytosines were found at CpA sites, particularly in hESCs (where CpA methylation represented >10% of methylcytosines). Levels of CpA methylation were lower in differentiated cells (with the lowest levels in monocytes, 2% of methylcytosines found at CpA sites). (C) In the HC sequence context, the position immediately 5′ of the methylcytosine did not appear to influence the methylation rate, as levels of methylation of the four categories of HC were equally distributed. (D,E) In the CHH sequence context, the predominant methylation type was CGH, followed by CAH. The position immediately 3′ to the dinucleotide had a weak effect on the methylation and was largely dependent on the identity of the second base of the dinucleotide.