We also identified megabase-scale genomic regions that were repeatedly resistant to reprogramming of non-CG methylation, and were associated with altered H3K9me3 and transcriptional activity, constituting phenotypic differences at the transcriptional level that could have downstream consequences for iPSC or derived somatic cell function. The close proximity of the non-CG mega-DMRs to centromeres and telomeres indicates that there could be distinct molecular properties of these chromosomal regions—for example particular histone variants—which impede the reprogramming process. Together, the non-CG mega-DMRs, common CG-DMRs in all iPSC lines, transmitted CG-DMRs and differentially expressed genes are potentially useful as diagnostic markers for incomplete iPSC reprogramming, characterization of the efficacy of different reprogramming techniques, and potential propagation of altered methylation states into derivative differentiated cells. From these first comprehensive whole-genome, base-resolution methylome maps it seems clear that iPSCs are fundamentally distinct from ES cells, insofar as they manifest common, quantifiable epigenomic differences. Continued study of a wide variety of ES cells is needed to understand the full range of epigenomic variability, and to potentially identify factors that enable complete reprogramming to occur.
