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Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells

Nature Cell Biology volume 13, pages 541–549 (2011)Cite this article

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Abstract

Human induced pluripotent stem (iPS) cells are remarkably similar to embryonic stem (ES) cells, but recent reports indicate that there may be important differences between them. We carried out a systematic comparison of human iPS cells generated from hepatocytes (representative of endoderm), skin fibroblasts (mesoderm) and melanocytes (ectoderm). All low-passage iPS cells analysed retain a transcriptional memory of the original cells. The persistent expression of somatic genes can be partially explained by incomplete promoter DNA methylation. This epigenetic mechanism underlies a robust form of memory that can be found in iPS cells generated by multiple laboratories using different methods, including RNA transfection. Incompletely silenced genes tend to be isolated from other genes that are repressed during reprogramming, indicating that recruitment of the silencing machinery may be inefficient at isolated genes. Knockdown of the incompletely reprogrammed gene C9orf64 (chromosome 9 open reading frame 64) reduces the efficiency of human iPS cell generation, indicating that somatic memory genes may be functionally relevant during reprogramming.

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Figure 1: Pluripotency validation for the derived Hep-iPS cells used for the microarray studies.
Figure 2: Multiple cell types undergo extensive transcriptional reprogramming to the human iPS cell state.
Figure 3: iPS cells retain a transcriptional memory of the original somatic cell.
Figure 4: DNA methylation can partially explain somatic gene expression in iPS cells.
Figure 5: Meta-analysis of DNA-methylation-associated transcriptional memory in independent data sets.
Figure 6: The somatic cell memory gene C9orf64 is required for efficient generation of iPS cells.
Figure 7: Proximity in the genome affects efficiency of gene silencing in iPS cells.
Figure 8: Model for the role of DNA methylation in reprogramming to the human iPS cell state.

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Acknowledgements

The authors wish to thank S. Fisher, O. Genbachev, A. Leavitt and B. Conklin for expert advice on culturing human ES cells, D. Subramanyam and R. Blelloch for the Adult Fibroblast-iPS 1 cell line, L. Ta, A. Williams and A. Holloway at the Gladstone Institutes, J. Bolen at the Mouse Pathology Core Facility for expert assistance, J. Utikal for technical advice, and J. Yang and A. Campain for sharing their meta-DEDS code. We thank members of the Santos laboratory, R. Blelloch, H. Willenbring, S. Fisher and M. Grskovic for helpful discussions and critical reading of the manuscript. Work in the Santos laboratory is supported by CIRM, JDRF, an NIH Director’s New Innovator Award and the Leona M. and Harry B. Helmsley Charitable Trust. Y.O. was partially supported by the UCSF Diabetes Center and a T32 grant from the NICHD to the UCSF Center for Reproductive Sciences. Work in M.H.’s laboratory was supported by grants from the JDRF and the Leona M. and Harry B. Helmsley Charitable Trust. T.G. was supported by the JDRF and the Leona M. and Harry B. Helmsley Charitable Trust. S.L.D. was partially supported by CIRM. J.S.S. was partially supported by the PhRMA Foundation.

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Author notes

  1. Yuki Ohi and Jun S. Song: These authors contributed equally to this work

Authors and Affiliations

  1. Departments of Ob/Gyn and Pathology and Center for Reproductive Sciences, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, USA

    Yuki Ohi, Han Qin, Laure Blouin & Miguel Ramalho-Santos

  2. Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, 35 Medical Center Way, San Francisco, California 94143, USA

    Yuki Ohi, Han Qin, Laure Blouin & Miguel Ramalho-Santos

  3. Diabetes Center, University of California, San Francisco, California 94143, USA

    Yuki Ohi, Han Qin, Laure Blouin, Tingxia Guo, Matthias Hebrok & Miguel Ramalho-Santos

  4. Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 Third Street, San Francisco, California 94158, USA

    Chibo Hong, Sara L. Downey & Joseph F. Costello

  5. Department of Medicine, Howard Hughes Medical Institute, Cancer Center and Center for Regenerative Medicine, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts 02114, USA

    Jose M. Polo & Konrad Hochedlinger

  6. Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138, USA

    Jose M. Polo, Philip D. Manos, Derrick J. Rossi & Konrad Hochedlinger

  7. Department of Medicine, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, USA

    Tingxia Guo & Matthias Hebrok

  8. Department of Laboratory Medicine, University of California San Francisco, 185 Berry Street, San Francisco, California 94107, USA

    Zhongxia Qi & Jingwei Yu

  9. Stem Cell Program, Children’s Hospital Boston, Boston, Massachusetts 02115, USA

    Philip D. Manos & Derrick J. Rossi

  10. Department of Pathology, Immune Disease Institute, Program in Cellular and Molecular Medicine, Children’s Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA

    Derrick J. Rossi

  11. Department of Epidemiology and Biostatistics, and Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, USA

    Jun S. Song

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  1. Yuki Ohi
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Contributions

Y.O., J.S.S. and M.R-S. conceived the project. J.M.P., K.H., P.D.M. and D.J.R. provided reagents. Z.Q. and J.Y. provided assistance with data analysis. C.H. and S.L.D. carried out the bisulphite sequencing analysis under supervision of J.F.C. T.G. carried out the targeted differentiation to endoderm analysis under supervision of M.H. J.S.S. carried out all of the bioinformatic analyses. Y.O., H.Q. and M.R-S. designed and Y.O. and H.Q. carried out all other experiments with technical assistance from L.B. Y.O, J.S.S. and M.R-S. wrote the manuscript with input from the other authors.

Corresponding authors

Correspondence to Jun S. Song or Miguel Ramalho-Santos.

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The authors declare no competing financial interests.

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Ohi, Y., Qin, H., Hong, C. et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol 13, 541–549 (2011). https://doi.org/10.1038/ncb2239

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