• A Corrigendum to this article was published on 01 October 2014

Abstract

Induced pluripotent stem cells (iPSCs) offer immense potential for regenerative medicine and studies of disease and development. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells. However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome. Here we report the first whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines, along with methylomes of ES cells, somatic cells, and differentiated iPSCs and ES cells. iPSCs show significant reprogramming variability, including somatic memory and aberrant reprogramming of DNA methylation. iPSCs share megabase-scale differentially methylated regions proximal to centromeres and telomeres that display incomplete reprogramming of non-CG methylation, and differences in CG methylation and histone modifications. Lastly, differentiation of iPSCs into trophoblast cells revealed that errors in reprogramming CG methylation are transmitted at a high frequency, providing an iPSC reprogramming signature that is maintained after differentiation.

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Accessions

Primary accessions

Sequence Read Archive

Data deposits

Analysed datasets can be browsed and downloaded from http://neomorph.salk.edu/ips_methylomes. Sequence data for MethylC-Seq, RNA-Seq and Chip-Seq experiments have been submitted to the NCBI SRA database under the accession numbers SRA023829.2 and SRP000941.

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Acknowledgements

We thank L. Zhang and G. Schroth for assistance with MethylC-Seq library sequencing. R.L. is supported by a California Institute for Regenerative Medicine Training Grant. M.P. is supported by a Catharina Foundation postdoctoral fellowship. R.D.H. is supported by an American Cancer Society Postdoctoral Fellowship. Y.K. is supported by the Japan Society for the Promotion of Science. This work was supported by grants from the following: Mary K. Chapman Foundation, the National Science Foundation (NSF) (NSF 0726408), the National Institutes of Health (NIH) (U01 ES017166, U01 1U01ES017166-01, DK062434), the California Institute for Regenerative Medicine (RB2-01530), the Morgridge Institute for Research and the Howard Hughes Medical Institute. We thank the NIH Roadmap Reference Epigenome Consortium (http://www.roadmapepigenomics.org/). This study was carried out as part of the NIH Roadmap Epigenomics Program.

Author information

Author notes

    • Ryan Lister
    •  & Mattia Pelizzola

    These authors contributed equally to this work.

Affiliations

  1. Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • Ryan Lister
    • , Mattia Pelizzola
    • , Joseph R. Nery
    • , Ronan O’Malley
    • , Rosa Castanon
    •  & Joseph R. Ecker
  2. Howard Hughes Medical Institute, Gene Expression laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • Yasuyuki S. Kida
    • , Michael Downes
    • , Ruth Yu
    •  & Ronald M. Evans
  3. Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA

    • R. David Hawkins
    • , Gary Hon
    • , Sarit Klugman
    •  & Bing Ren
  4. Morgridge Institute for Research, Madison, Wisconsin 53707, USA

    • Jessica Antosiewicz-Bourget
    • , Ron Stewart
    •  & James A. Thomson
  5. Genome Center of Wisconsin, Madison, Wisconsin 53706, USA

    • Jessica Antosiewicz-Bourget
    • , Ron Stewart
    •  & James A. Thomson
  6. Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA

    • Bing Ren
  7. Wisconsin National Primate Research Center, University of Wisconsin—Madison, Madison, Wisconsin 53715, USA

    • James A. Thomson
  8. Department of Anatomy, University of Wisconsin—Madison, Madison, Wisconsin 53706, USA

    • James A. Thomson

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Contributions

Experiments were designed by R.L., J.R.E., R.M.E., B.R., J.A.T., Y.S.K., R.Y., M.D. and R.D.H. Cells were grown by J.A.-B. and Y.S.K. MethylC-Seq and RNA-Seq experiments were conducted by R.L. and J.R.N. ChIP-Seq experiments were conducted by R.D.H. ChIP-Seq data analysis was performed by G.H., S.K. and R.D.H. Retroviral insertion site localization experiments were performed by R.O’M. and R.C. Sequencing data processing was performed by R.L. and G.H. Bioinformatic and statistical analyses were conducted by M.P., R.L. and G.H. R.S. performed data interpretation analyses. The manuscript was prepared by R.L., M.P. and J.R.E.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Joseph R. Ecker.

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DOI

https://doi.org/10.1038/nature09798

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