Several lines of evidence support a mechanistic link between differential methylation and hematopoietic propensity of iPSC lines. First, literature survey of genes for the top 24 DMRs that distinguish B-iPSC and F-iPSC links 11 to hematopoiesis and 3 to osteogenesis (Supplementary Table 2). Of the 11 hematopoietic loci, 10 are hypermethylated in F-iPSC relative to B-iPSC. Second, of 74 hematopoietic transcription factors23, 20 are in or near DMRs that are hypermethylated in F-iPSC versus B-iPSC, twice that predicted by chance (p=0.0034; Fig. 3b left panel, Supplementary Fig. 3a, and Supplementary Table 3). Similarly, of 764 fibroblast-specific genes, 115 are hypermethylated in B-iPSC, twice that predicted by chance (p=10−5; Fig 3b right panel). Given the correlation between methylation and transcriptional silencing24, our data suggest that iPSC harbor epigenetic marks antagonistic to cell lineages distinct from the donor cell type.
