Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Epigenetic memory in induced pluripotent stem cells

Nature volume 467, pages 285–290 (2010)Cite this article

Subjects

Abstract

Somatic cell nuclear transfer and transcription-factor-based reprogramming revert adult cells to an embryonic state, and yield pluripotent stem cells that can generate all tissues. Through different mechanisms and kinetics, these two reprogramming methods reset genomic methylation, an epigenetic modification of DNA that influences gene expression, leading us to hypothesize that the resulting pluripotent stem cells might have different properties. Here we observe that low-passage induced pluripotent stem cells (iPSCs) derived by factor-based reprogramming of adult murine tissues harbour residual DNA methylation signatures characteristic of their somatic tissue of origin, which favours their differentiation along lineages related to the donor cell, while restricting alternative cell fates. Such an ‘epigenetic memory’ of the donor tissue could be reset by differentiation and serial reprogramming, or by treatment of iPSCs with chromatin-modifying drugs. In contrast, the differentiation and methylation of nuclear-transfer-derived pluripotent stem cells were more similar to classical embryonic stem cells than were iPSCs. Our data indicate that nuclear transfer is more effective at establishing the ground state of pluripotency than factor-based reprogramming, which can leave an epigenetic memory of the tissue of origin that may influence efforts at directed differentiation for applications in disease modelling or treatment.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Pluripotent stem cells and their characterization.
Figure 2: Differentiation of cell lines.
Figure 3: Analysis of methylation in stem cell lines.
Figure 4: Stringently defined pluripotent stem cells and their characterization.

Similar content being viewed by others

Article 01 December 2022

Zixuan Zhao, Xinyi Chen, … Hanry Yu

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

CHARM microarray data are deposited at the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession number GSE22851.

References

  1. Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006)

    Article  CAS  Google Scholar 

  2. Zhao, X. Y. et al. iPS cells produce viable mice through tetraploid complementation. Nature 461, 86–90 (2009)

    Article  CAS  ADS  Google Scholar 

  3. Daley, G. Q. et al. Broader implications of defining standards for the pluripotency of iPSCs. Cell Stem Cell 4, 200–201 (2009)

    Article  CAS  Google Scholar 

  4. Marión, R. M. et al. A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity. Nature 460, 1149–1153 (2009)

    Article  ADS  Google Scholar 

  5. Li, H. et al. The Ink4/Arf locus is a barrier for iPS cell reprogramming. Nature 460, 1136–1139 (2009)

    Article  CAS  ADS  Google Scholar 

  6. Eminli, S. et al. Differentiation stage determines potential of hematopoietic cells for reprogramming into induced pluripotent stem cells. Nature Genet. 41, 968–976 (2009)

    Article  CAS  Google Scholar 

  7. Gurdon, J. B. & Melton, D. A. Nuclear reprogramming in cells. Science 322, 1811–1815 (2008)

    Article  CAS  ADS  Google Scholar 

  8. Blelloch, R. et al. Reprogramming efficiency following somatic cell nuclear transfer is influenced by the differentiation and methylation state of the donor nucleus. Stem Cells 24, 2007–2013 (2006)

    Article  CAS  Google Scholar 

  9. Maherali, N. et al. A high-efficiency system for the generation and study of human induced pluripotent stem cells. Cell Stem Cell 3, 340–345 (2008)

    Article  CAS  Google Scholar 

  10. Aoi, T. et al. Generation of pluripotent stem cells from adult mouse liver and stomach cells. Science 321, 699–702 (2008)

    Article  CAS  ADS  Google Scholar 

  11. Miura, K. et al. Variation in the safety of induced pluripotent stem cell lines. Nature Biotechnol. 27, 743–745 (2009)

    Article  CAS  Google Scholar 

  12. Chan, E. M. et al. Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells. Nature Biotechnol. 27, 1033–1037 (2009)

    Article  CAS  Google Scholar 

  13. Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49–55 (2008)

    Article  CAS  ADS  Google Scholar 

  14. Santos, F., Hendrich, B., Reik, W. & Dean, W. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev. Biol. 241, 172–182 (2002)

    Article  CAS  Google Scholar 

  15. Skow, L. C. et al. A mouse model for β-thalassemia. Cell 34, 1043–1052 (1983)

    Article  CAS  Google Scholar 

  16. Kyba, M., Perlingeiro, R. C. & Daley, G. Q. HoxB4 confers definitive lymphoid-myeloid engraftment potential on embryonic stem cell and yolk sac hematopoietic progenitors. Cell 109, 29–37 (2002)

    Article  CAS  Google Scholar 

  17. Bourne, S., Polak, J. M., Hughes, S. P. & Buttery, L. D. Osteogenic differentiation of mouse embryonic stem cells: differential gene expression analysis by cDNA microarray and purification of osteoblasts by cadherin-11 magnetically activated cell sorting. Tissue Eng. 10, 796–806 (2004)

    Article  CAS  Google Scholar 

  18. Wdziekonski, B., Villageois, P. & Dani, C. Differentiation of mouse embryonic stem cells and of human adult stem cells into adipocytes. Curr. Protoc. Cell Biol. 23, 23.24 (2007)

    Google Scholar 

  19. Hood, R. C. & Neill, W. M. A modification of alizarin red S technic for demonstrating bone formation. Stain Technol. 23, 209–218 (1948)

    Article  CAS  Google Scholar 

  20. Irizarry, R. A. et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18, 780–790 (2008)

    Article  CAS  Google Scholar 

  21. Irizarry, R. A. et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nature Genet. 41, 178–186 (2009)

    Article  CAS  Google Scholar 

  22. Doi, A. et al. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nature Genet. 41, 1350–1353 (2009)

    Article  CAS  Google Scholar 

  23. Turker, M. S. Gene silencing in mammalian cells and the spread of DNA methylation. Oncogene 21, 5388–5393 (2002)

    Article  CAS  Google Scholar 

  24. Perez-Iratxeta, C. et al. Study of stem cell function using microarray experiments. FEBS Lett. 579, 1795–1801 (2005)

    Article  CAS  Google Scholar 

  25. Kim, J., Chu, J., Shen, X., Wang, J. & Orkin, S. H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049–1061 (2008)

    Article  CAS  Google Scholar 

  26. Wernig, M. et al. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature 448, 318–324 (2007)

    Article  CAS  ADS  Google Scholar 

  27. Wernig, M. et al. A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types. Nature Biotechnol. 26, 916–924 (2008)

    Article  CAS  Google Scholar 

  28. Hanna, J. et al. Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell 133, 250–264 (2008)

    Article  CAS  Google Scholar 

  29. Brambrink, T., Hochedlinger, K., Bell, G. & Jaenisch, R. ES cells derived from cloned and fertilized blastocysts are transcriptionally and functionally indistinguishable. Proc. Natl Acad. Sci. USA 103, 933–938 (2006)

    Article  CAS  ADS  Google Scholar 

  30. Eggan, K. et al. Hybrid vigor, fetal overgrowth, and viability of mice derived by nuclear cloning and tetraploid embryo complementation. Proc. Natl Acad. Sci. USA 98, 6209–6214 (2001)

    Article  CAS  ADS  Google Scholar 

  31. Nadin, B. M., Goodell, M. A. & Hirschi, K. K. Phenotype and hematopoietic potential of side population cells throughout embryonic development. Blood 102, 2436–2443 (2003)

    Article  CAS  Google Scholar 

  32. Eden, S., Hashimshony, T., Keshet, I., Cedar, H. & Thorne, A. W. DNA methylation models histone acetylation. Nature 394, 842 (1998)

    Article  CAS  ADS  Google Scholar 

  33. Chiu, C. P. & Blau, H. M. 5-Azacytidine permits gene activation in a previously noninducible cell type. Cell 40, 417–424 (1985)

    Article  CAS  Google Scholar 

  34. Lengerke, C. et al. BMP and Wnt specify hematopoietic fate by activation of the Cdx-Hox pathway. Cell Stem Cell 2, 72–82 (2008)

    Article  CAS  Google Scholar 

  35. Ball, M. P. et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nature Biotechnol. 27, 361–368 (2009)

    Article  CAS  ADS  Google Scholar 

  36. Kim, J. B. et al. Oct4-induced pluripotency in adult neural stem cells. Cell 136, 411–419 (2009)

    Article  CAS  Google Scholar 

  37. Loh, Y. H. et al. Generation of induced pluripotent stem cells from human blood. Blood 113, 5476–5479 (2009)

    Article  CAS  Google Scholar 

  38. Chin, M. H. et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 5, 111–123 (2009)

    Article  CAS  Google Scholar 

  39. Hanna, J. et al. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462, 595–601 (2009)

    Article  CAS  ADS  Google Scholar 

  40. Okita, K., Ichisaka, T. & Yamanaka, S. Generation of germline-competent induced pluripotent stem cells. Nature 448, 313–317 (2007)

    Article  CAS  ADS  Google Scholar 

  41. Soldner, F. et al. Parkinson’s disease patient-derived induced pluripotent stem cells free of viral reprogramming factors. Cell 136, 964–977 (2009)

    Article  CAS  Google Scholar 

  42. Stadtfeld, M. et al. Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature 465, 175–181 (2010)

    Article  CAS  ADS  Google Scholar 

  43. Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006)

    Article  CAS  Google Scholar 

  44. Xu, J. et al. Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes Dev. 23, 2824–2838 (2009)

    Article  CAS  Google Scholar 

  45. Osafune, K. et al. Marked differences in differentiation propensity among human embryonic stem cell lines. Nature Biotechnol. 26, 313–315 (2008)

    Article  CAS  Google Scholar 

  46. Silva, J. et al. Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol. 6, e253 (2008)

    Article  Google Scholar 

  47. Polo, J. M. et al. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nature Biotechnol. 10.1038/nbt.1667 (19 July 2010)

  48. Nomizu, T. et al. Determination of calcium content in individual biological cells by inductively coupled plasma atomic emission spectrometry. Anal. Chem. 66, 3000–3004 (1994)

    Article  CAS  Google Scholar 

  49. Kirov, G. et al. Variation in the protocadherin γ A gene cluster. Genomics 82, 433–440 (2003)

    Article  CAS  Google Scholar 

  50. Markoulaki, S. et al. Transgenic mice with defined combinations of drug-inducible reprogramming factors. Nature Biotechnol. 27, 169–171 (2009)

    Article  CAS  Google Scholar 

  51. Koh, E. Y., Chen, T. & Daley, G. Q. Novel retroviral vectors to facilitate expression screens in mammalian cells. Nucleic Acids Res. 30, e142 (2002)

    Article  Google Scholar 

  52. Conti, L. et al. Niche-independent symmetrical self-renewal of a mammalian tissue stem cell. PLoS Biol. 3, e283 (2005)

    Article  Google Scholar 

  53. Schiedlmeier, B. et al. HOXB4’s road map to stem cell expansion. Proc. Natl Acad. Sci. USA 104, 16952–16957 (2007)

    Article  CAS  ADS  Google Scholar 

  54. Pavlidis, P. & Noble, W. S. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol. 2, RESEARCH0042 (2001)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

G.Q.D is an investigator of the Howard Hughes Medical Institute and was supported by NIH grants RO1-DK70055 and RO1-DK59279, and special funds received under the American Recovery and Reinvestment Act (RC2-HL102815). K.K. was supported by NIH (K99HL093212-01), LLS (3567-07) and Cooley’s Anemia Foundation. A.P.F was funded by NIH grants R37CA054358 and P50HG003233. I.L.W. was funded by NIH grants R01AI047457, R01AI047458, CA86065 and HL099999, and the Thomas and Stacey Siebel Foundation. L.I.R.E. was supported by a Special Fellow Career Development award from the Leukemia and Lymphoma Society. J.S. is supported by a fellowship from the California Institute for Regenerative Medicine (T1-00001). We acknowledge K. Hochedlinger for sharing his manuscript before publication.

Author information

Author notes

  1. L. I. R. Ehrlich & T. J. Yoon

    Present address: Present addresses: University of Texas at Austin, Molecular Genetics and Microbiology, 2506 Speedway, NMS 2.314, Austin, Texas 78712, USA (L.I.R.E.); Department of Applied Bioscience, CHA University, Seoul 135-081, Korea (T.J.Y.).,

Authors and Affiliations

  1. Division of Pediatric Hematology/Oncology, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Stem Cell Transplantation Program, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Harvard Medical School; Harvard Stem Cell Institute,

    K. Kim, K. Ng, R. Zhao, P. Cahan, A. Yabuuchi, A. Takeuchi, K. C. Cunniff, H. Hongguang, S. Mckinney-Freeman, O. Naveiras & G. Q. Daley

  2. Division of Hematology, Brigham and Women’s Hospital, Boston, 02115, Massachusetts, USA

    K. Kim, K. Ng, R. Zhao, P. Cahan, A. Yabuuchi, A. Takeuchi, K. C. Cunniff, H. Hongguang, S. Mckinney-Freeman, O. Naveiras & G. Q. Daley

  3. Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland, USA

    A. Doi, B. Wen, H. Ji, R. A. Irizarry, N. Jung, P. Murakami & A. P. Feinberg

  4. Department of Pediatric Oncology, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute,

    J. Kim & S. H. Orkin

  5. Boston, 02115, Massachusetts, USA

    J. Kim & S. H. Orkin

  6. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, 21205, Maryland, USA

    M. J. Aryee

  7. Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, 94305, California, USA

    L. I. R. Ehrlich, J. Seita & I. L. Weissman

  8. Center for Systems Biology, Massachusetts General Hospital/Harvard Medical School, 185 Cambridge Street, CPZN 5206, Boston, Massachusetts 02114, USA,

    T. J. Yoon & R. Weissleder

  9. Department of Biology, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, 02142, Massachusetts, USA

    J. Hanna & R. Jaenisch

Authors
  1. K. Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. Doi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. B. Wen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. K. Ng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. R. Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. P. Cahan
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. J. Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. M. J. Aryee
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. H. Ji
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. L. I. R. Ehrlich
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. A. Yabuuchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. A. Takeuchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. K. C. Cunniff
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. H. Hongguang
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. S. Mckinney-Freeman
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. O. Naveiras
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. T. J. Yoon
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. R. A. Irizarry
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. N. Jung
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. J. Seita
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. J. Hanna
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. P. Murakami
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. R. Jaenisch
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. R. Weissleder
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. S. H. Orkin
    View author publications

    You can also search for this author in PubMed Google Scholar

  26. I. L. Weissman
    View author publications

    You can also search for this author in PubMed Google Scholar

  27. A. P. Feinberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  28. G. Q. Daley
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

K.K. and G.Q.D. conceived the experimental plan. K.K., A.D., B.W., K.N., Z.R., H.J., L.I.R.E., A.Y., A.T., K.C.C., H.H., S.M.-F., O.N., T.J.Y., R.A.I., N.J., J.S., J.H. and P.M. performed the experiments. P.C., J.K. and M.J.A. performed statistical analysis. A.D., B.W. and A.P.F. performed CHARM and guided analysis of methylation. K.K., A.D., B.W., K.N., R.Z., P.C., J.K., M.J.A., H.J., T.J.Y., R.J., R.W., S.H.O., I.L.W., A.P.F. and G.Q.D. wrote the manuscript.

Corresponding authors

Correspondence to A. P. Feinberg or G. Q. Daley.

Ethics declarations

Competing interests

G.Q.D. is a member of the Scientific Advisory Boards of MPM Capital, Inc., Epizyme, Inc., and iPierian, Inc. R.J. is a member of the Scientific Advisory Boards of Fate Therapeutics, Inc. and StemGent, Inc. I.L.W is a member of the Scientific Advisory Boards of Cellerant, Inc, and Stem Cells, Inc.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-13 with legends, Supplementary Tables 1-7 and References. (PDF 8512 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kim, K., Doi, A., Wen, B. et al. Epigenetic memory in induced pluripotent stem cells. Nature 467, 285–290 (2010). https://doi.org/10.1038/nature09342

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature09342

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing