Consistent with our previous results, DNA hypomethylation was the most discriminate epigenetic feature of any given tissue (Figure 2A, Table S3). For a majority of these tissue-specific groups of hypomethylated genes, functional enrichments using GREAT were also consistent with the particular tissue’s function and/or cellular composition (Figure 2B). Interestingly, approximately 20% (2,554/12,254) of these hypomethylated CpGs were associated with transcription factors (according to region-gene associations in GREAT). Among these, CpGs associated with POU5F1 and NANOG, which are known master regulators of pluripotency and are among the six transcription factors commonly used in reprogramming, were hypomethylated specifically in hPSCs (Figure 2C). Additionally, CpGs associated with the neural lineage transcription factors MYT1L, POU3F3, SOX1, and MYT1 were specifically hypomethylated in brain samples. In fact, MYT1L is one of four required factors for the direct conversion of fibroblasts into neurons (Pang et al., 2011) and POU3F3 (BRN1) is a closely related functional homolog of another neuronal transdifferentiation factor, POU3F2 (BRN2) (Figure 2C).
