Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types (original) (raw)
Figure 3
CpA methylation dynamics are closely linked to DNMT3 gene expression levels.
(A) Number of CpAs (y-axis; value ×104) methylated (≥5% methylation) in various somatic cell types and median number of methylated CpAs in EBs. Median number of methylated CpAs in a representative subset of ESCs (n = 11) is shown as reference. Whiskers indicate 25th and 75th quartiles. (B) Distribution of CpA methylation levels in 7 pluripotent cell samples and matching 16 day EBs (top). Boxes are 25th and 75th quartiles, whiskers indicate most extreme data point less than 1.5 interquartile range from box and black bar represents the median. Below are normalized absolute log2 gene expression levels of DNMT3A, DNMT3B and OCT4 in the corresponding samples (measured using Affymetrix GeneChip HT HG-U133A microarrays; Table S1). Left sample in each pair corresponds to the undifferentiated state and right sample to the matching EB state. (C) Distribution of CpG methylation levels in 7 pluripotent cell lines and matching 16 day EBs. (D) CpA methylation levels of various genomic region classes in ESC line H1p38 and matching 16 EBs. (E) CpA methylation levels of various genomic region classes in iPSC line 27e matching day 16 EBs.