the vast majority of them (119 of 130, or 92%) were hypomethylated in the iPSC lines, indicating that the general deficiency in resetting DNA methylation patterns during reprogramming is insufficient methylation. Notably, the remaining 11 CG-DMRs hypermethylated in all iPSC lines were iDMRs, as they are not differentially methylated in the progenitor cells compared to the ES cells. In addition, they were associated with transcriptional repression and the absence of the heterochromatic H3K27me3 histone modification, compared to H1 ES cells (Fig. 4a, b).
