Abstract
Induced pluripotent stem (iPS) cells are derived by epigenetic reprogramming, but their DNA methylation patterns have not yet been analyzed on a genome-wide scale. Here, we find substantial hypermethylation and hypomethylation of cytosine-phosphate-guanine (CpG) island shores in nine human iPS cell lines as compared to their parental fibroblasts. The differentially methylated regions (DMRs) in the reprogrammed cells (denoted R-DMRs) were significantly enriched in tissue-specific (T-DMRs; 2.6-fold, P < 10−4) and cancer-specific DMRs (C-DMRs; 3.6-fold, P < 10−4). Notably, even though the iPS cells are derived from fibroblasts, their R-DMRs can distinguish between normal brain, liver and spleen cells and between colon cancer and normal colon cells. Thus, many DMRs are broadly involved in tissue differentiation, epigenetic reprogramming and cancer. We observed colocalization of hypomethylated R-DMRs with hypermethylated C-DMRs and bivalent chromatin marks, and colocalization of hypermethylated R-DMRs with hypomethylated C-DMRs and the absence of bivalent marks, suggesting two mechanisms for epigenetic reprogramming in iPS cells and cancer.
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Acknowledgements
This research was supported by the US National Institutes of Health (A.P.F. and G.Q.D.). G.Q.D affiliations include the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; the Division of Hematology, Brigham and Women's Hospital; Harvard Stem Cell Institute; and the Manton Center for Orphan Disease Research.
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A.D. performed CHARM, bisulfite pyrosequencing and data analysis; B.W. performed initial experiments and helped design and analyze the study; I.-H.P., J.R., S.L., J.M. and T.S. performed cell culture and prepared nucleic acids; P.M., M.J.A., R.I., B.H. and C.L.-A. performed statistical analysis; G.Q.D. and A.P.F. designed the study, supervised the experiments and wrote the paper with A.D. and B.W.
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Supplementary Text and Figures
Supplementary Figures 1–3, Supplementary Tables 3–4, 7,9–10 (PDF 1297 kb)
Supplementary Table 1
Reprogramming differentially methylated regions (R-DMRs). (XLS 914 kb)
Supplementary Table 2
Gene ontology functional categories enriched in reprogramming differentially methylated regions (R-DMRs). (XLS 47 kb)
Supplementary Table 5
Regions of differential methylation between 3 additional iPS lines and the fibroblasts from which they were derived. (XLS 424 kb)
Supplementary Table 6
Regions of differential methylation between iPS cells and ES cells. (XLS 32 kb)
Supplementary Table 8
Relationship between differential gene expression and differential methylation at reprogramming differentially methylated regions (R-DMRs). (XLS 131 kb)
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Doi, A., Park, IH., Wen, B. et al. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 41, 1350–1353 (2009). https://doi.org/10.1038/ng.471
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DOI: https://doi.org/10.1038/ng.471
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