Based on the observation of tissue-specific patterns of DNA hypomethylation and the assumption that epigenetic patterns in hPSCs represent those of the early human embryo, we reasoned that DNA demethylation was a normal component of cellular differentiation. To test this hypothesis, we profiled three hPSC lines before and after in vitro directed differentiation into NESTIN/PAX6+ neural progenitor cells (NPCs; Figure 3A) and mixed populations of A2B5/OLIG1+ oligodendroctye precursor cells (OPCs; Figure 3B) and GALC+ oligodendrocytes (Figure 3C) using established methods (Harness et al., 2011; Nistor et al., 2005). Using 1,303 CpGs that were differentially methylated in OPCs or NPCs compared to hPSCs and to all non-brain tissues, hierarchical clustering of these differentiated samples, hPSCs, and tissues clearly distinguished NPCs, OPCs and brain samples from hPSCs and all other tissues (Table S4, Figure S2A). Demethylation of several genes known to regulate oligodendrocyte differentiation including SKI, QKI, and OLIG2 (Aberg et al., 2006; Atanasoski et al., 2004; Zhou and Anderson, 2002) and the myelin proteins PLP1 and PMP22 (Figure 3D) was observed and reflected in the GREAT enrichments for myelination and regulation
