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Naive embryonic stem cells hold great promise for research and therapeutics as they have broad and robust developmental potential. While such cells are readily derived from mouse blastocysts it has not been possible to isolate human equivalents easily1,2, although human naive-like cells have been artificially generated (rather than extracted) by coercion of human primed embryonic stem cells by modifying culture conditions2,3,4 or through transgenic modification5. Here we show that a sub-population within cultures of human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) manifests key properties of naive state cells. These naive-like cells can be genetically tagged, and are associated with elevated transcription of HERVH, a primate-specific endogenous retrovirus. HERVH elements provide functional binding sites for a combination of naive pluripotency transcription factors, including LBP9, recently recognized as relevant to naivety in mice6. LBP9–HERVH drives hESC-specific alternative and chimaeric transcripts, including pluripotency-modulating long non-coding RNAs. Disruption of LBP9, HERVH and HERVH-derived transcripts compromises self-renewal. These observations define HERVH expression as a hallmark of naive-like hESCs, and establish novel primate-specific transcriptional circuitry regulating pluripotency.

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Change history

  • 17 December 2014

    Cell line hiPS-SK4 was corrected to hFF-iPS4 in Fig. 1, Methods and the Acknowledgements.


Primary accessions

Gene Expression Omnibus

Data deposits

RNA-seq and microarray data were submitted to NCBI’s GEO database under accession GSE54726.


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L.D.H. is Wolfson Royal Society Research Merit Award Holder. A.T.G. is funded by a scholarship from the University of Bath. Z.Iz. is funded by ERC-2011-AdG 294742. G.G.S. is funded by DFG grant SCHU1014/8-1 and LOEWE Center for Cell and Gene Therapy Frankfurt/Hessian Ministry of Higher Education, Research and the Arts (ref. number III L 4-518/17.004). We thank U. Martin and S. Merkert (Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School, Hannover, Germany) for providing the cell lines hCBEC, hCBiPS1, hCBiPS2 and hFF-iPS4. We thank G. Klein for the inspiration of working with ERVs and Z. Cseresnyés for his assistance in imaging.

Author information

Author notes

    • Jichang Wang
    •  & Gangcai Xie

    These authors contributed equally to this work.


  1. Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany

    • Jichang Wang
    • , Gangcai Xie
    • , Manvendra Singh
    • , Tamás Raskó
    • , Attila Szvetnik
    • , Huiqiang Cai
    • , Daniel Besser
    • , Alessandro Prigione
    • , Nina V. Fuchs
    • , Wei Chen
    •  & Zsuzsanna Izsvák
  2. Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yueyang Road, Shanghai 200031, China

    • Gangcai Xie
  3. University of Bath, Department of Biology and Biochemistry, Bath, Somerset BA2 7AY, UK

    • Avazeh T. Ghanbarian
    •  & Laurence D. Hurst
  4. Paul-Ehrlich-Institute, Division of Medical Biotechnology, Paul-Ehrlich-Strasse 51-59, 63225 Langen, Germany

    • Nina V. Fuchs
    • , Gerald G. Schumann
    •  & Zoltán Ivics
  5. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada

    • Matthew C. Lorincz


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This project was inspired by M.C.L. Z.Iz., L.D.H. and J.W. conceived ideas for the project, and wrote the manuscript with contributions from other authors. The project was supervised by Z.Iz. and L.D.H. Z.Iv. provided critical advice. J.W. designed and performed experiments, analysed and interpreted data, and participated in bioinformatic analyses. T.R. contributed by EMSA and assisted in immunostaining experiments. A.S. assisted in the reporter assays. H.C. assisted in shRNA cloning. W.C. and J.W. performed RNA-seq experiments. A.P. provided materials and performed karyotype analysis. D.B., N.V.F. and G.G.S. provided materials. G.X. performed RNA-seq, bisulfite-seq and ChIP-seq analyses. M.S. analysed microarray data and performed cross-species correlation studies. L.D.H. and A.T.G. performed all the other bioinformatic analyses.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Laurence D. Hurst or Zsuzsanna Izsvák.

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    Supplementary Information

    This file contains a Supplementary Discussion and Supplementary References.

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    This file contains Supplementary Tables 1-16 and a Supplementary Table Guide.

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    This file contains an html rendering of alignment of the intron containing ESRG, as well as human ESRG, across multiple primates.


  1. 1.

    Spatial structure visualization of the naïve state GFP(high) cells in a dome shaped hESC_H9 colony.

    The colonies are genetically marked with GFP and immunostained with NANOG. Red, NANOG; green, GFP; blue, DAPI (nucleus); scare bar, 20 μM. Layer scanning was performed and images were taken using a Leica LSM710 point--‐scanning single photon confocal microscope. 3D image movies construction were created by Imaris Imaging Software (Bitplane). The colony shows mESC--‐like morphology (3D, multilayer). Note that high GFP fluorescence and NANOG staining appears in the same cells.

  2. 2.

    Spatial structure visualization of the naïve state GFP(high) cells in a mosaic hESC_H9 colony.

    The colonies are genetically marked with GFP and immunostained with NANOG. Red, NANOG; green, GFP; blue, DAPI (nucleus); scare bar, 20 μM. Layer scanning was performed and images were taken using a Leica LSM710 point--‐scanning single photon confocal microscope. 3D image movies construction were created by Imaris Imaging Software (Bitplane). The mosaic colony shows typical hESC morphology (2D, monolayer).

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