Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Control of ground-state pluripotency by allelic regulation of Nanog


Pluripotency is established through genome-wide reprogramming during mammalian pre-implantation development, resulting in the formation of the naive epiblast. Reprogramming involves both the resetting of epigenetic marks and the activation of pluripotent-cell-specific genes such as Nanog and Oct4 (also known as Pou5f1)1,2,3,4. The tight regulation of these genes is crucial for reprogramming, but the mechanisms that regulate their expression in vivo have not been uncovered. Here we show that Nanog—but not Oct4—is monoallelically expressed in early pre-implantation embryos. Nanog then undergoes a progressive switch to biallelic expression during the transition towards ground-state pluripotency in the naive epiblast of the late blastocyst. Embryonic stem (ES) cells grown in leukaemia inhibitory factor (LIF) and serum express Nanog mainly monoallelically and show asynchronous replication of the Nanog locus, a feature of monoallelically expressed genes5, but ES cells activate both alleles when cultured under 2i conditions, which mimic the pluripotent ground state in vitro. Live-cell imaging with reporter ES cells confirmed the allelic expression of Nanog and revealed allelic switching. The allelic expression of Nanog is regulated through the fibroblast growth factor–extracellular signal-regulated kinase signalling pathway, and it is accompanied by chromatin changes at the proximal promoter but occurs independently of DNA methylation. Nanog-heterozygous blastocysts have fewer inner-cell-mass derivatives and delayed primitive endoderm formation, indicating a role for the biallelic expression of Nanog in the timely maturation of the inner cell mass into a fully reprogrammed pluripotent epiblast. We suggest that the tight regulation of Nanog dose at the chromosome level is necessary for the acquisition of ground-state pluripotency during development. Our data highlight an unexpected role for allelic expression in controlling the dose of pluripotency factors in vivo, adding an extra level to the regulation of reprogramming.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: Nanog expression is monoallelic in early embryos.
Figure 2: Nanog shows biallelic expression in the naive, pluripotent epiblast.
Figure 3: The switch to biallelic expression of Nanog is accompanied by changes in replication timing and increased recruitment of mediator and cohesin.
Figure 4: Biallelic expression of Nanog is required for the timely maturation of the ICM derivatives.


  1. Mitsui, K. et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113, 631–642 (2003)

    Article  CAS  Google Scholar 

  2. Chambers, I. et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 113, 643–655 (2003)

    Article  CAS  Google Scholar 

  3. Nichols, J. et al. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95, 379–391 (1998)

    Article  CAS  Google Scholar 

  4. Reik, W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425–432 (2007)

    Article  ADS  CAS  Google Scholar 

  5. Gribnau, J., Hochedlinger, K., Hata, K., Li, E. & Jaenisch, R. Asynchronous replication timing of imprinted loci is independent of DNA methylation, but consistent with differential subnuclear localization. Genes Dev. 17, 759–773 (2003)

    Article  CAS  Google Scholar 

  6. Silva, J. et al. Nanog is the gateway to the pluripotent ground state. Cell 138, 722–737 (2009)

    Article  CAS  Google Scholar 

  7. Dietrich, J. E. & Hiiragi, T. Stochastic patterning in the mouse pre-implantation embryo. Development 134, 4219–4231 (2007)

    Article  CAS  Google Scholar 

  8. Nichols, J., Silva, J., Roode, M. & Smith, A. Suppression of Erk signalling promotes ground state pluripotency in the mouse embryo. Development 136, 3215–3222 (2009)

    Article  CAS  Google Scholar 

  9. Morrisey, E. E., Ip, H. S., Lu, M. M. & Parmacek, M. S. GATA-6: a zinc finger transcription factor that is expressed in multiple cell lineages derived from lateral mesoderm. Dev. Biol. 177, 309–322 (1996)

    Article  CAS  Google Scholar 

  10. Chambers, I. et al. Nanog safeguards pluripotency and mediates germline development. Nature 450, 1230–1234 (2007)

    Article  ADS  CAS  Google Scholar 

  11. Kalmar, T. et al. Regulated fluctuations in Nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol. 7, e1000149 (2009)

    Article  Google Scholar 

  12. Ying, Q. L. et al. The ground state of embryonic stem cell self-renewal. Nature 453, 519–523 (2008)

    Article  ADS  CAS  Google Scholar 

  13. Wray, J., Kalkan, T. & Smith, A. G. The ground state of pluripotency. Biochem. Soc. Trans. 38, 1027–1032 (2010)

    Article  CAS  Google Scholar 

  14. Canham, M. A., Sharov, A. A., Ko, M. S. & Brickman, J. M. Functional heterogeneity of embryonic stem cells revealed through translational amplification of an early endodermal transcript. PLoS Biol. 8, e1000379 (2010)

    Article  Google Scholar 

  15. Weaver, J. R., Susiarjo, M. & Bartolomei, M. S. Imprinting and epigenetic changes in the early embryo. Mamm. Genome 20, 532–543 (2009)

    Article  Google Scholar 

  16. Shufaro, Y. et al. Reprogramming of DNA replication timing. Stem Cells 28, 443–449 (2010)

    CAS  PubMed  Google Scholar 

  17. Jørgensen, H. F. et al. The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells. Genome Biol. 8, R169 (2007)

    Article  Google Scholar 

  18. Magklara, A. et al. An epigenetic signature for monoallelic olfactory receptor expression. Cell 145, 555–570 (2011)

    Article  CAS  Google Scholar 

  19. Tsumura, A. et al. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 11, 805–814 (2006)

    Article  CAS  Google Scholar 

  20. Kagey, M. H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430–435 (2010)

    Article  ADS  CAS  Google Scholar 

  21. Messerschmidt, D. M. & Kemler, R. Nanog is required for primitive endoderm formation through a non-cell autonomous mechanism. Dev. Biol. 344, 129–137 (2010)

    Article  CAS  Google Scholar 

  22. Hough, S. R., Clements, I., Welch, P. J. & Wiederholt, K. A. Differentiation of mouse embryonic stem cells after RNA interference-mediated silencing of OCT4 and Nanog. Stem Cells 24, 1467–1475 (2006)

    Article  CAS  Google Scholar 

  23. Hatano, S. Y. et al. Pluripotential competence of cells associated with Nanog activity. Mech. Dev. 122, 67–79 (2005)

    Article  CAS  Google Scholar 

  24. Bolzer, A. et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 3, e157 (2005)

    Article  Google Scholar 

  25. Lewis, A. et al. Epigenetic dynamics of the Kcnq1 imprinted domain in the early embryo. Development 133, 4203–4210 (2006)

    Article  CAS  Google Scholar 

  26. Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005)

    Article  CAS  Google Scholar 

  27. Sage, D., Unser, M., Salmon, P. & Dibner, C. A software solution for recording circadian oscillator features in time-lapse live cell microscopy. Cell Div. 5, 17 (2010)

    Article  Google Scholar 

Download references


We thank M. Okano for providing the triple DNA methyltransferase knockout cells, P. Avner and P. Clerc for hybrid ES cells, H. Schöler for the Oct4 probe (GOF6.1), J. Jaubert for M. musculus castaneus mice, R. Kemler and S. Rudloff for the NanogGt1mice, G. Charvin for advice on time-lapse analysis. We also thank M. Koch, A. Dierich, M.-C. Birling, E. Heard and I. Okamoto for advice, and A. Burton, E. Heard and O. Pourquie for critical reading of the manuscript. M.-E.T.-P. acknowledges funding from AVENIR/INSERM, ANR-09-Blanc-0114, Epigenesys NoE and FRM Alsace. Y.M. is a recipient of an EMBO long-term fellowship (ALTF864-2008, 2009) and a JSPS postdoctoral fellowship (2010–2011).

Author information

Authors and Affiliations



Y.M. conceived, designed and performed the experiments in this study and analysed the data; M.-E.T.-P. conceived the project and designed and supervised the study. Y.M. and M.-E. T.-P wrote the manuscript.

Corresponding author

Correspondence to Maria-Elena Torres-Padilla.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-8 with legends and Supplementary Table 1. (PDF 3671 kb)

Supplementary Movie 1

This movie shows serial confocal sections (0.3 μm step) of 4-cell stage embryos. Nascent transcripts of Nanog (yellow) and Oct4 (red) were detected by RNA-FISH. DNA was stained with DAPI in blue. (MOV 8251 kb)

Supplementary Movie 2

This movie shows serial confocal sections (0.3 μm step) of ICM cells of late blastocyst. Nascent transcript of Nanog (yellow) was visualized by RNA-FISH. DNA was stained with DAPI in blue. (MOV 3143 kb)

Supplementary Movie 3

This movie shows serial confocal sections (0.3 μm step) of ES cells cultured with serum and LIF. Nascent transcripts of Nanog (yellow) and Oct4 (red) were visualized by RNA-FISH. DNA was stained with DAPI in blue. (MOV 1437 kb)

Supplementary Movie 4

This movie shows serial confocal sections (0.3 μm step) of ES cells cultured with 2i. Nascent transcripts of Nanog (yellow) and Oct4 (red) were visualized by RNA-FISH. DNA was stained with DAPI in blue. (MOV 2637 kb)

Supplementary Movie 5

This movie shows time-lapse imaging of NGR ES cells cultured in medium containing LIF. Images are acquired along 7 Z-planes spanning 17.5 μm every 20 min for 38 hrs under a spinning disk confocal. Series of maximum intensity projection at each time point is converted to the movie. (MOV 9482 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Miyanari, Y., Torres-Padilla, ME. Control of ground-state pluripotency by allelic regulation of Nanog. Nature 483, 470–473 (2012).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing