The CpG sites in the PluripotentLowVar/SomaticLowVar category were separated into seven clusters by hierarchical clustering (Figure 1A). Each cluster was tested for functional enrichments using the Genomic Regions Enrichment of Annotations Tool (GREAT (McLean et al., 2010)), but only one cluster showed significant enrichments. This cluster was fully methylated in pluripotent samples, partially methylated in somatic samples and was significantly enriched for genes associated with purinergic nucleotide receptor activity and genomic imprinting. The enrichment of imprinted regions in this group demonstrates that a subset of imprinted genes is consistently hypermethylated in hPSCs relative to somatic samples, suggesting a difference in the regulation of imprinted genes between hPSCs and somatic cells. DNA methylation and gene expression were anti-correlated (R < −0.50) for many of these genes (Figure S1A–B).
