Figure 4

Levels of DNA methylation and demethylation enzymes and overlap of aberrantly methylated regions with genomic binding sites of reprogramming factors. A. Expression levels of enzymes involved in methylation and demethylation in pluripotent cells measured using qPCR. Data is log2 transformed and normalized to levels of these enzymes in human fibroblasts. Values shown are the mean of the following number of samples: n = 2 (ESCs), n = 3 (Y-iPSCs) and n = 3 (T-iPSCs). B and C. Random sampling simulation to determine the distribution of the expected number of genes that are targets of the indicated reprogramming factor and have aberrant DNA methylation CpGs overlapping the binding site. The histograms and box plots represent the null distribution for the overlap between random sampling DNA methylation aberrations and each transcription factor binding sites. The diamonds represent the experimentally observed number of overlap between Y-iPSCs (B) or T-iPSCs (C) DNA methylation aberrations and each transcription factor binding sites. Red diamonds highlight a number of overlaps that fall completely outside of the null distribution.