• A Corrigendum to this article was published on 17 June 2015

This article has been updated

Abstract

Somatic cell reprogramming to a pluripotent state continues to challenge many of our assumptions about cellular specification, and despite major efforts, we lack a complete molecular characterization of the reprograming process. To address this gap in knowledge, we generated extensive transcriptomic, epigenomic and proteomic data sets describing the reprogramming routes leading from mouse embryonic fibroblasts to induced pluripotency. Through integrative analysis, we reveal that cells transition through distinct gene expression and epigenetic signatures and bifurcate towards reprogramming transgene-dependent and -independent stable pluripotent states. Early transcriptional events, driven by high levels of reprogramming transcription factor expression, are associated with widespread loss of histone H3 lysine 27 (H3K27me3) trimethylation, representing a general opening of the chromatin state. Maintenance of high transgene levels leads to re-acquisition of H3K27me3 and a stable pluripotent state that is alternative to the embryonic stem cell (ESC)-like fate. Lowering transgene levels at an intermediate phase, however, guides the process to the acquisition of ESC-like chromatin and DNA methylation signature. Our data provide a comprehensive molecular description of the reprogramming routes and is accessible through the Project Grandiose portal at http://www.stemformatics.org.

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Change history

  • 10 December 2014

    A minor addition was made to the Acknowledgements in the HTML and PDF versions.

Accessions

Primary accessions

European Nucleotide Archive

Sequence Read Archive

Data deposits

Sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) under accession number SRP046744 for all RNA-seq and ChIP-seq experiments, and in the European Bioinformatics Institute under the European Nucleotide Archive (ENA) accession number ERP004116 for MethylC-sequencing. The global and cell surface mass spectrometry proteomics raw data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository under data set identifiers PXD000413 and PXD001456, respectively.

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Acknowledgements

We thank M. Gertsenstein and M. Pereira for chimaera production, C. Monetti for cell culture, R. Cowling for DNA purification, and K. Harpal for chimaera embryo sectioning and staining. We acknowledge the intellectual contributions of P. P. L. Tam and R. P. Harvey. A.N. is Tier 1 Canada Research Chair in Stem Cells and Regeneration. This work was supported by grants awarded to A.N., I.M.R. and P.W.Z. from the Ontario Research Fund Global Leadership Round in Genomics and Life Sciences grants (GL2-01-028), to A.N. from the Canadian stem cell network (9/5254 (TR3)) and from the Canadian Institutes of Health Research (CIHR MOP102575). This work received support from the Korean Ministry of Knowledge Economy (grant 10037410 to J.-S.S.), from the SNUCM Research Fund (grant 0411-20100074 to J.-S.S.), and from Macrogen Inc. (grant MGR03-11 and MGR03-12). The Stemformatics resource is supported by an Australian Research Council special research grant to Stem Cells Australia (C.A.W. and S.M.G.). The analysis of the miRNA was supported by grants from the National Health and Medical Research Council of Australia (1024852 to J.L.C. and T.P.) and the Australian Research Council (DP1300101928 to T.P.). W.R. is a Cancer Institute of NSW Fellow and with J.E.J.R. receives support from the Cancer Council of NSW and National Health & Medical Research Council (571156 and 1061906). J.E.J.R. receives funding from Cure the Future & Tour de Cure. K.-A.L.C. is supported, in part, by the Wound Management Innovation CRC (established and supported under the Australian Government’s Cooperative Research Centres Program). S.M.G. received support from the Australian Research Council (SR110001002). C.A.W. is a QLD Smart Futures Fellow. M.B., J.M. and A.J.R.H. are supported by the Netherlands Proteomics Centre, and by the European Community’s Seventh Framework Programme (FP7/2007-2013) by the PRIME-XS project grant agreement number 262067. P.W.Z. is the Canada Research Chair in Stem Cell Bioengineering. S.M.I.H. received a fellowship from the McEwen Centre of Regenerative Medicine.

Author information

Author notes

    • Samer M. I. Hussein
    • , Mira C. Puri
    •  & Peter D. Tonge

    These authors contributed equally to this work.

    • Javier Munoz
    •  & Kim-Anh Lê Cao

    Present addresses: Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain (J.M.); The University of Queensland Diamantina Institute, Translational Research Institute, 37 Kent Street, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia (K.-A.L.C.).

Affiliations

  1. Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada

    • Samer M. I. Hussein
    • , Mira C. Puri
    • , Peter D. Tonge
    • , Andrew J. Corso
    • , Mira Li
    • , Ian M. Rogers
    •  & Andras Nagy
  2. Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5T 3H7, Canada

    • Mira C. Puri
  3. Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands

    • Marco Benevento
    • , Javier Munoz
    •  & Albert J. R. Heck
  4. Netherlands Proteomics Centre, Padualaan 8, 3584CH Utrecht, The Netherlands

    • Marco Benevento
    • , Javier Munoz
    •  & Albert J. R. Heck
  5. Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 3H7, Canada

    • Andrew J. Corso
    •  & Andras Nagy
  6. Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra), ACT 2601, Australia

    • Jennifer L. Clancy
    • , Hardip R. Patel
    •  & Thomas Preiss
  7. Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia

    • Rowland Mosbergen
    • , Othmar Korn
    •  & Christine A. Wells
  8. Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, South Korea

    • Dong-Sung Lee
    • , Jong-Yeon Shin
    • , Jong-Il Kim
    •  & Jeong-Sun Seo
  9. Department of Biomedical Sciences and Biochemistry, Seoul National University College of Medicine, Seoul 110-799, South Korea

    • Dong-Sung Lee
    • , Jong-Il Kim
    •  & Jeong-Sun Seo
  10. Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia

    • Nicole Cloonan
    • , David L. A. Wood
    • , Maely E. Gauthier
    • , Kim-Anh Lê Cao
    •  & Sean M. Grimmond
  11. Gene and Stem Cell Therapy Program and Bioinformatics Lab, Centenary Institute, Camperdown 2050, NSW, Australia & Sydney Medical School, 31 University of Sydney 2006, New South Wales, Australia

    • Robert Middleton
    • , William Ritchie
    •  & John E. J. Rasko
  12. Genome Discovery Unit, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra) 2601, ACT, Australia

    • Hardip R. Patel
  13. Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto M5S-3G9, Canada

    • Carl A. White
    • , Nika Shakiba
    •  & Peter W. Zandstra
  14. The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto M5S 3E1, Canada

    • Carl A. White
    •  & Peter W. Zandstra
  15. Life Science Institute, Macrogen Inc., Seoul 153-781, South Korea

    • Jong-Yeon Shin
    •  & Jeong-Sun Seo
  16. Department of Systems & Computational Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA

    • Jessica C. Mar
  17. Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, New South Wales, Australia

    • John E. J. Rasko
  18. College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK

    • Christine A. Wells
  19. Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia

    • Thomas Preiss
  20. Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada

    • Ian M. Rogers
  21. Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario M5S 1E2, Canada

    • Ian M. Rogers
    •  & Andras Nagy
  22. QIMR Berghofer Medical Research Institute, Genomic Biology Lab, 300 Herston Road, Herston, Queensland 4006, Australia

    • Nicole Cloonan

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Contributions

S.M.I.H., M.C.P., P.D.T. and A.N. conceived, designed and carried out most of the experiments, interpreted results and wrote the manuscript. P.W.Z. contributed to study design. T.P., C. A. Wells, I.M.R., P.W.Z., C. A. White, N.S., A.J.C. and J.C.M. assisted with data interpretation and manuscript writing. M.L., S.M.I.H. and M.C.P. performed ChIP. M.C.P., S.M.I.H., N.C., O.K., D.L.A.W., M.E.G. and S.M.G. produced and analysed RNA-seq data. S.M.I.H., D.-S.L., M.C.P., J.-Y.S., J.-I.K. and J.-S.S. produced and analysed MethylC-seq and ChIP-seq data. J.E.J.R, W.R. and R.Mi. performed the IR analysis, interpretation and contributed to the manuscript writing. C. A. Wells, R.Mo., O.K., K.-A.LC. and J.C.M. provided support for bioinformatics analyses and data visualization. M.B., J.M. and A.J.R.H. performed the LC-MS analysis and proteomic data analysis. H.R.P. mapped the miRNA Next Generation Sequencing (NGS) data and provided support for bioinformatics analyses and data visualization. J.L.C. and T.P. analysed and interpreted the miRNA NGS data. C.A.W. performed the CSC proteomics. C.A.W., N.S. and P.W.Z. analysed CSC proteome data.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Andras Nagy.

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