• A Corrigendum to this article was published on 28 February 2018

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The foundations of mammalian development lie in a cluster of embryonic epiblast stem cells. In response to extracellular matrix signalling, these cells undergo epithelialization and create an apical surface in contact with a cavity1,2, a fundamental event for all subsequent development. Concomitantly, epiblast cells transit through distinct pluripotent states3,4, before lineage commitment at gastrulation. These pluripotent states have been characterized at the molecular level5, but their biological importance remains unclear. Here we show that exit from an unrestricted naive pluripotent state is required for epiblast epithelialization and generation of the pro-amniotic cavity in mouse embryos. Embryonic stem cells locked in the naive state are able to initiate polarization but fail to undergo lumenogenesis. Mechanistically, exit from naive pluripotency activates an Oct4-governed transcriptional program that results in expression of glycosylated sialomucin proteins and the vesicle tethering and fusion events of lumenogenesis. Similarly, exit of epiblasts from naive pluripotency in cultured human post-implantation embryos triggers amniotic cavity formation and developmental progression. Our results add tissue-level architecture as a new criterion for the characterization of different pluripotent states, and show the relevance of transitions between these states during development of the mammalian embryo.

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  • 28 February 2018

    Please see accompanying Erratum (http://doi.org/10.1038/nature25995). Extended Data Fig. 4 has been replaced, to correct the missing colours in the key to panels c, h, k, n and q, and to correct the missing colours of the graph in panel k.


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We thank K. McNagny, J. Hanna and R. Jaenisch for reagents and discussions; F. Martin-Belmonte, D. Glover, C. Lynch, M. Serrano, A. Hupalowska, F. Antonica and M. Petruzzelli for feedback; J. N. Skepper for help with electron microscopy; W. Mansfield for help with embryo transfer. This work was supported by Wellcome Trust (098287/Z/12/Z) and ERC (669198) grants to M.Z.-G. Work in the laboratory of T.V. was supported by Wellcome Trust and KU Leuven (SymBioSys PFV/10/016). Work in the laboratory of J.C.M. was supported by EMBL and Cancer Research UK. M.N.S. was supported by Ramon Areces and EMBO postdoctoral fellowships; A.S. by a Wellcome Trust strategic award (105031/D/14/Z) and G.R. by a Newton fellowship.

Author information

Author notes

    • Antonio Scialdone
    • , Gaelle Recher
    • , Iain C. Macaulay
    •  & Christa Buecker

    Present addresses: Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München 85764, Germany (A.S.); Bioimaging and Optofluidics group, IOGS, CNRS & University of Bordeaux, Rue Francois Mitterrand, 33400 Talence, France (G.R.); Earlham Institute, Norwich Research Park, Norwich NR4 7UG, UK (I.C.M.); Max F. Perutz Laboratories, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, Vienna 1030, Austria (C.B.).


  1. Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3EG, UK.

    • Marta N. Shahbazi
    • , Natalia Skorupska
    • , Antonia Weberling
    • , Gaelle Recher
    • , Meng Zhu
    • , Agnieszka Jedrusik
    •  & Magdalena Zernicka-Goetz
  2. EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK.

    • Antonio Scialdone
    •  & John C. Marioni
  3. Faculty of Life Sciences and Medicine, King’s College London, Women’s Health Academic Centre, Assisted Conception Unit, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK.

    • Liani G. Devito
    • , Laila Noli
    • , Yakoub Khalaf
    •  & Dusko Ilic
  4. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.

    • Iain C. Macaulay
    • , Thierry Voet
    •  & John C. Marioni
  5. Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA.

    • Christa Buecker
  6. Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Herestraat 49, Leuven 3000, Belgium.

    • Thierry Voet
  7. Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.

    • John C. Marioni


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M.N.S. designed, performed and analysed most of the experiments. A.S. analysed the sequencing data. N.S. and A.W. performed experiments in Fig. 4g and Extended Data Figs 57. M.Z. and G.R. helped with embryo experiments and image analysis. A.J., L.G.D. and L.N. helped with human embryo cultures. I.C.M. prepared cDNA libraries. C.B. generated and analysed ChIP–seq data. D.I. and Y.K. supervised the human embryo experiments. T.V. supervised the cDNA library preparation. J.C.M. supervised the computational analyses of the sequencing data. M.Z.-G. supervised the study. M.N.S. and M.Z.-G. conceived the project and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Magdalena Zernicka-Goetz.

Reviewer Information Nature thanks J.-L. Maitre and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Life Sciences Reporting Summary

  2. 2.

    Supplementary Table 2

    This file contains antibodies used in this study.

  3. 3.

    Supplementary Table 3

    This file contains a list of RT-PCR primers used in this study.

Excel files

  1. 1.

    Supplementary Table 1

    This file contains genes expressed in the mouse epiblast at peri-implantation stages.


  1. 1.

    ΔPE-Oct4-GFP mESCs cultured in 3D matrigel without 2i/LIF and imaged every 30 minutes.

    The arrow points to the cell shown in Extended Data Fig. 2e. The maximum projection is shown throughout the movie. Scale bars, 50 μm.

  2. 2.

    Rex1::GFPd2 mESCs cultured in 3D matrigel without 2i/LIF and imaged every 30 minutes.

    The arrow points to the cell shown in Extended Data Fig. 2e. The maximum projection is shown throughout the movie. Scale bars, 50 μm.

  3. 3.

    Nanog-YFP mTmG mESCs cultured in 3D matrigel without 2i/LIF and imaged every 30 minutes.

    The arrow points to the cell shown in Extended Data Fig. 2e. The maximum projection is shown throughout the movie. Scale bars, 50 μm.

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