Article | Published:

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

Nature volume 487, pages 5763 (05 July 2012) | Download Citation

Abstract

Embryonic stem (ES) cells are derived from blastocyst-stage embryos and are thought to be functionally equivalent to the inner cell mass, which lacks the ability to produce all extraembryonic tissues. Here we identify a rare transient cell population within mouse ES and induced pluripotent stem (iPS) cell cultures that expresses high levels of transcripts found in two-cell (2C) embryos in which the blastomeres are totipotent. We genetically tagged these 2C-like ES cells and show that they lack the inner cell mass pluripotency proteins Oct4 (also known as Pou5f1), Sox2 and Nanog, and have acquired the ability to contribute to both embryonic and extraembryonic tissues. We show that nearly all ES cells cycle in and out of this privileged state, which is partially controlled by histone-modifying enzymes. Transcriptome sequencing and bioinformatic analyses showed that many 2C transcripts are initiated from long terminal repeats derived from endogenous retroviruses, suggesting this foreign sequence has helped to drive cell-fate regulation in placental mammals.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

Data deposits

Microarray and RNA-seq files have been submitted to the NCBI Gene Expression Omnibus database under accession GSE33923.

References

  1. 1.

    Experiments on the development of isolated blastomers of mouse eggs. Nature 184, 1286–1287 (1959)

  2. 2.

    , & Development and phenotypic variability of genetically identical half mouse embryos. Development 106, 817–827 (1989)

  3. 3.

    & Making the blastocyst: lessons from the mouse. J. Clin. Invest. 120, 995–1003 (2010)

  4. 4.

    & Embryonic genome activation. Front. Biosci. 6, d748–d759 (2001)

  5. 5.

    The molecular foundations of the maternal to zygotic transition in the preimplantation embryo. Hum. Reprod. Update 8, 323–331 (2002)

  6. 6.

    Gene expression and chromatin structure in the pre-implantation embryo. Theriogenology 59, 3–19 (2003)

  7. 7.

    & Establishment in culture of pluripotential cells from mouse embryos. Nature 292, 154–156 (1981)

  8. 8.

    Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl Acad. Sci. USA 78, 7634–7638 (1981)

  9. 9.

    & An assessment of the developmental potential of embryonic stem cells in the midgestation mouse embryo. Development 105, 733–737 (1989)

  10. 10.

    et al. Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes Dev. 24, 312–326 (2010)

  11. 11.

    , , & Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states. Cell Stem Cell 3, 391–401 (2008)

  12. 12.

    , , & A heterogeneous expression pattern for Nanog in embryonic stem cells. Stem Cells 25, 2534–2542 (2007)

  13. 13.

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

  14. 14.

    et al. Zscan4 regulates telomere elongation and genomic stability in ES cells. Nature 464, 858–863 (2010)

  15. 15.

    et al. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7, 597–606 (2004)

  16. 16.

    et al. Systems biology of the 2-cell mouse embryo. Cytogenet. Genome Res. 105, 240–250 (2004)

  17. 17.

    , , & MuERV-L is one of the earliest transcribed genes in mouse one-cell embryos. Biol. Reprod. 68, 651–654 (2003)

  18. 18.

    et al. RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos. Dev. Biol. 269, 276–285 (2004)

  19. 19.

    et al. Murine endogenous retrovirus MuERV-L is the progenitor of the “orphan” epsilon viruslike particles of the early mouse embryo. J. Virol. 82, 1622–1625 (2008)

  20. 20.

    et al. Targeted mutagenesis of the transcription factor GATA-4 gene in mouse embryonic stem cells disrupts visceral endoderm differentiation in vitro. Development 121, 3877–3888 (1995)

  21. 21.

    et al. Transcription factor TEAD4 specifies the trophectoderm lineage at the beginning of mammalian development. Development 134, 3827–3836 (2007)

  22. 22.

    et al. Tead4 is required for specification of trophectoderm in pre-implantation mouse embryos. Mech. Dev. 125, 270–283 (2008)

  23. 23.

    , , , & In silico mining of EST databases for novel pre-implantation embryo-specific zinc finger protein genes. Mol. Reprod. Dev. 59, 249–255 (2001)

  24. 24.

    , , , & TDPOZ, a family of bipartite animal and plant proteins that contain the TRAF (TD) and POZ/BTB domains. Gene 324, 117–127 (2004)

  25. 25.

    et al. Zfp206 regulates ES cell gene expression and differentiation. Nucleic Acids Res. 34, 4780–4790 (2006)

  26. 26.

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

  27. 27.

    , , & Regulation of zygotic gene activation in the preimplantation mouse embryo: global activation and repression of gene expression. Biol. Reprod. 64, 1713–1721 (2001)

  28. 28.

    , , & Changes in histone synthesis and modification at the beginning of mouse development correlate with the establishment of chromatin mediated repression of transcription. J. Cell Sci. 110, 1147–1158 (1997)

  29. 29.

    et al. Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev. 25, 594–607 (2011)

  30. 30.

    et al. KAP1 controls endogenous retroviruses in embryonic stem cells. Nature 463, 237–240 (2010)

  31. 31.

    et al. G9a selectively represses a class of late-replicating genes at the nuclear periphery. Proc. Natl Acad. Sci. USA 106, 19363–19368 (2009)

  32. 32.

    , , & Zygotically activated genes are suppressed in mouse nuclear transferred embryos. Cloning Stem Cells 8, 295–304 (2006)

  33. 33.

    et al. Effect of trychostatin A treatment on gene expression in cloned mouse embryos. Theriogenology 71, 1245–1252 (2009)

  34. 34.

    et al. Generation of human-induced pluripotent stem cells in the absence of exogenous Sox2. Stem Cells 27, 2992–3000 (2009)

  35. 35.

    et al. Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells. Sci. Rep. 2, 208 (2012)

  36. 36.

    Transposable elements and the evolution of regulatory networks. Nature Rev. Genet. 9, 397–405 (2008)

  37. 37.

    et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nature Genet. 42, 631–634 (2010)

  38. 38.

    , , & Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nature Genet. 43, 1154–1159 (2011)

  39. 39.

    et al. Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene. Proc. Natl Acad. Sci. USA 106, 12127–12132 (2009)

  40. 40.

    , , , & ERV-L elements: a family of endogenous retrovirus-like elements active throughout the evolution of mammals. J. Virol. 73, 3301–3308 (1999)

  41. 41.

    & Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010)

  42. 42.

    , & Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44–57 (2009)

Download references

Acknowledgements

We would like to thank members of the Pfaff laboratory for discussion; S. Andrews, D. Chambers, Y. Dayn, T.-C. Sung, J. Fitzpatrick, M. Joens, Y. Sigal, D. Gibbs and L. Ouyang for technical assistance, Y. Shinkai and D. Gilbert for the G9a mutant ES cells, and T. Heidmann for MuERV-L-Gag antibodies. This research was supported by the National Institute of Neurological Disorders and Stroke (R37NS037116) and the Marshall Heritage Foundation. T.S.M. and W.D.G. were supported by the California Institute for Regenerative Medicine and S.L.P. is an investigator of the Howard Hughes Medical Institute and Benjamin H. Lewis Chair in Neurobiology.

Author information

Author notes

    • Todd S. Macfarlan

    Present address: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.

Affiliations

  1. Howard Hughes Medical Institute, Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines, La Jolla, California 92037, USA

    • Todd S. Macfarlan
    • , Wesley D. Gifford
    • , Shawn Driscoll
    • , Karen Lettieri
    • , Dario Bonanomi
    •  & Samuel L. Pfaff
  2. School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland

    • Helen M. Rowe
    •  & Didier Trono
  3. Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines, La Jolla, California 92037, USA

    • Amy Firth
    •  & Oded Singer

Authors

  1. Search for Todd S. Macfarlan in:

  2. Search for Wesley D. Gifford in:

  3. Search for Shawn Driscoll in:

  4. Search for Karen Lettieri in:

  5. Search for Helen M. Rowe in:

  6. Search for Dario Bonanomi in:

  7. Search for Amy Firth in:

  8. Search for Oded Singer in:

  9. Search for Didier Trono in:

  10. Search for Samuel L. Pfaff in:

Contributions

T.S.M. designed and performed all experiments with assistance from W.D.G., S.D., D.B. and K.L. under the supervision of S.L.P. D.T. generated Kap1 mutant ES cells and H.M.R. and D.T. provided mRNA-seq data from these cells. A.F. and O.S. generated and provided iPS cell lines and lentivirus constructs. T.S.M., W.D.G. and S.L.P. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Samuel L. Pfaff.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Figures 1-11 and legends for Supplementary Movies 1-3.

Zip files

  1. 1.

    Supplementary Tables

    This zipped file contains Supplementary Tables 1-7.

Videos

  1. 1.

    Supplementary Movie 1

    The 2C::tomato reporter is restricted to the zygote and 2C/4C stage - see Supplementary Information fie for full legend.

  2. 2.

    Supplementary Movie 2

    2C::tomato is transiently expressed in ES cultures - see Supplementary Information fie for full legend.

  3. 3.

    Supplementary Movie 3

    Entrance into the 2C::tomato (+) state is more rapid in Kdm1a mutant ES cells - see Supplementary Information fie for full legend.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature11244

Further reading

Comments

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.