Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells (original) (raw)

• Article
• Published: 02 February 2011
• Mattia Pelizzola1 na1,
• Yasuyuki S. Kida2,
• R. David Hawkins3,
• Joseph R. Nery1,
• Gary Hon3,
• Jessica Antosiewicz-Bourget4,5,
• Ronan O’Malley1,
• Rosa Castanon1,
• Sarit Klugman3,
• Michael Downes2,
• Ruth Yu2,
• Ron Stewart4,5,
• Bing Ren3,6,
• James A. Thomson4,5,7,8,
• Ronald M. Evans2 &
• …
• Joseph R. Ecker1

Nature volume 471, pages 68–73 (2011)Cite this article

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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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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.

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Author notes

1. Ryan Lister and Mattia Pelizzola: These authors contributed equally to this work.

Authors and Affiliations

1. Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, 92037, California, 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, 92037, California, USA
   Yasuyuki S. Kida, Michael Downes, Ruth Yu & Ronald M. Evans
3. Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, 92093, California, USA
   R. David Hawkins, Gary Hon, Sarit Klugman & Bing Ren
4. Morgridge Institute for Research, Madison, 53707, Wisconsin, USA
   Jessica Antosiewicz-Bourget, Ron Stewart & James A. Thomson
5. Genome Center of Wisconsin, Madison, 53706, Wisconsin, USA
   Jessica Antosiewicz-Bourget, Ron Stewart & James A. Thomson
6. Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093, California, USA
   Bing Ren
7. Wisconsin National Primate Research Center, University of Wisconsin—Madison, Madison, 53715, Wisconsin, USA
   James A. Thomson
8. Department of Anatomy, University of Wisconsin—Madison, Madison, 53706, Wisconsin, USA
   James A. Thomson

Authors

1. Ryan Lister
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2. Mattia Pelizzola
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3. Yasuyuki S. Kida
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4. R. David Hawkins
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5. Joseph R. Nery
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6. Gary Hon
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7. Jessica Antosiewicz-Bourget
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8. Ronan O’Malley
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9. Rosa Castanon
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10. Sarit Klugman
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11. Michael Downes
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12. Ruth Yu
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13. Ron Stewart
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14. Bing Ren
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15. James A. Thomson
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16. Ronald M. Evans
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17. Joseph R. Ecker
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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.

Corresponding author

Correspondence toJoseph R. Ecker.

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The authors declare no competing financial interests.

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Lister, R., Pelizzola, M., Kida, Y. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.Nature 471, 68–73 (2011). https://doi.org/10.1038/nature09798

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• Received: 11 September 2010
• Accepted: 11 January 2011
• Published: 02 February 2011
• Issue Date: 03 March 2011
• DOI: https://doi.org/10.1038/nature09798

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Editorial Summary

Genetic abnormalities in iPS cells

Epigenomic reprogramming of somatic cells to produce iPS (induced pluripotent stem) cells has important therapeutic potential and is the basis of potentially important disease models. Recent reports that the reprogramming and in vitro culture of iPS cells can induce genetic and epigenetic abnormalities raise concerns over the implications of these abnormalities for clinical applications of iPS cells. Three papers in this issue present genomics studies of human iPS and embryonic stem (ES) cells, and taken together, the results confirm that chromosomal, subchromosomal and single-base level anomalies do accumulate in iPS cells. Hussein et al. compare copy number alterations of early and intermediate passage human iPS cells and report a higher level of copy number variations associated with reprogramming. During moderate length culture, however, iPS cells undergo a selection process leading to a decreased mutation load equivalent to that seen in ES cells. Gore et al. report protein-coding point mutations in 22 human iPS cell lines reprogrammed using five different methods; some mutations were pre-existing in the somatic cells, others were new mutations linked to reprogramming. Lister et al. used whole-genome DNA methylation profiling of human ES, iPS and somatic progenitor cell lines to reveal 'hotspots' in the genomes of iPS cells that are aberrantly reprogrammed.

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