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Naive pluripotency is associated with global DNA hypomethylation

Nature Structural & Molecular Biology volume 20, pages 311–316 (2013)Cite this article

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Abstract

Naive pluripotent embryonic stem cells (ESCs) and embryonic germ cells (EGCs) are derived from the preimplantation epiblast and primordial germ cells (PGCs), respectively. We investigated whether differences exist between ESCs and EGCs, in view of their distinct developmental origins. PGCs are programmed to undergo global DNA demethylation; however, we find that EGCs and ESCs exhibit equivalent global DNA methylation levels. Inhibition of MEK and Gsk3b by 2i conditions leads to pronounced reduction in DNA methylation in both cell types. This is driven by Prdm14 and is associated with downregulation of Dnmt3a and Dnmt3b. However, genomic imprints are maintained in 2i, and we report derivation of EGCs with intact genomic imprints. Collectively, our findings establish that culture in 2i instills a naive pluripotent state with a distinctive epigenetic configuration that parallels molecular features observed in both the preimplantation epiblast and nascent PGCs.

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Figure 1: Culture environment defines the transcriptional profile of pluripotent stem cells.
Figure 2: Global DNA hypomethylation in 2i.
Figure 3: Characteristics of DNA methylation changes between culture conditions.
Figure 4: Prdm14 regulates DNA methylation in pluripotent stem cells.
Figure 5: Imprinted DMR methylation status of ESC and EGC lines.
Figure 6: Naive pluripotency is characterized by DNA hypomethylation.

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  • 24 February 2013

    In the version of this article initially published online, a bar connecting the two central data sets in Figure 3e was inadvertently included. The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

We thank members of the Smith, Surani and Hajkova labs for stimulating discussions and C. Mulas for comments on the manuscript. We are also grateful to B. Snijders from the Medical Research Council (MRC) Clinical Sciences Centre Proteomics facility and Agilent Technologies for their support regarding the LC-MS analysis. Affymetrix array hybridization and quality control was carried out by the Genomics Laboratory at the MRC Clinical Sciences Centre. A.S. is supported as an MRC Professor. This work was supported by MRC funding to P.H. (MC A652 5PY70) as well as a Wellcome Trust grant to M.A.S. (RG49135) and MRC funding to A.S. (G1001028).

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Author notes

  1. Harry G Leitch and Kirsten R McEwen: These authors contributed equally to this work.

Authors and Affiliations

  1. Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK

    Harry G Leitch, Nils Grabole, William Mansfield, Austin Smith & M Azim Surani

  2. Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, UK

    Harry G Leitch, Nils Grabole & M Azim Surani

  3. Medical Research Council Clinical Sciences Centre, Imperial College London, London, UK.,

    Kirsten R McEwen, Aleksandra Turp, Vesela Encheva, Tom Carroll, Buhe Nashun & Petra Hajkova

  4. Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK

    Nils Grabole, Jaysen G Knezovich & M Azim Surani

  5. Department of Biochemistry, University of Cambridge, Cambridge, UK

    Austin Smith

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Contributions

The study was conceived of and designed by H.G.L., K.R.M. and P.H. Experiments were performed by H.G.L., K.R.M., A.T., V.E., B.N. and P.H. Bioinformatic analysis was performed by T.C. and K.R.M. Blastocyst injections were performed by W.M., N.G. and J.G.K. provided reagents. A.S. and M.A.S. provided critical feedback. H.G.L., K.R.M. and P.H. wrote the manuscript.

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Correspondence to Petra Hajkova.

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Leitch, H., McEwen, K., Turp, A. et al. Naive pluripotency is associated with global DNA hypomethylation. Nat Struct Mol Biol 20, 311–316 (2013). https://doi.org/10.1038/nsmb.2510

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