XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells (original) (raw)

Nature Genetics volume 45, pages 239–241 (2013)Cite this article

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Abstract

X-chromosome inactivation (XCI) in mammals relies on XIST, a long noncoding transcript that coats and silences the X chromosome in cis. Here we report the discovery of a long noncoding RNA, XACT, that is expressed from and coats the active X chromosome specifically in human pluripotent cells. In the absence of XIST, XACT is expressed from both X chromosomes in humans but not in mice, suggesting a unique role for XACT in the control of human XCI initiation.

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References

  1. Guttman, M. et al. Nature 458, 223–227 (2009).
    Article CAS Google Scholar
  2. Khalil, A.M. et al. Proc. Natl. Acad. Sci. USA 106, 11667–11672 (2009).
    Article CAS Google Scholar
  3. Augui, S., Nora, E.P. & Heard, E. Nat. Rev. Genet. 12, 429–442 (2011).
    Article CAS Google Scholar
  4. Dvash, T. & Fan, G. Epigenetics 4, 19–22 (2009).
    Article CAS Google Scholar
  5. The ENCODE Project Consortium. PLoS Biol. 9, e1001046 (2011).
  6. Romanish, M.T., Lock, W.M., van de Lagemaat, L.N., Dunn, C.A. & Mager, D.L. PLoS Genet. 3, e10 (2007).
    Article Google Scholar
  7. Sandelin, A. et al. Nat. Rev. Genet. 8, 424–436 (2007).
    Article CAS Google Scholar
  8. Silva, S.S., Rowntree, R.K., Mekhoubad, S. & Lee, J.T. Proc. Natl. Acad. Sci. USA 105, 4820–4825 (2008).
    Article CAS Google Scholar
  9. Mekhoubad, S. et al. Cell Stem Cell 10, 595–609 (2012).
    Article CAS Google Scholar
  10. Mitjavila-Garcia, M.T. et al. J. Mol. Cell Biol. 2, 291–298 (2010).
    Article CAS Google Scholar
  11. Shen, Y. et al. Proc. Natl. Acad. Sci. USA 105, 4709–4714 (2008).
    Article CAS Google Scholar
  12. Giuliani, M. et al. Blood 118, 3254–3262 (2011).
    Article CAS Google Scholar
  13. Okamoto, I. et al. Nature 472, 370–374 (2011).
    Article CAS Google Scholar
  14. Okamoto, I., Otte, A.P., Allis, C.D., Reinberg, D. & Heard, E. Science 303, 644–649 (2004).
    Article CAS Google Scholar
  15. Rougeulle, C. & Avner, P. Semin. Cell Dev. Biol. 14, 331–340 (2003).
    Article CAS Google Scholar

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Acknowledgements

We thank members of our laboratory and M. Lalande for stimulating discussion and critical reading of the manuscript. The research leading to these results has received funding from the European Research Council (ERC) under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement 206875 and the INSERM (Avenir Program R0721HS).

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Authors and Affiliations

  1. Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, Paris, France
    Céline Vallot, Christophe Huret & Claire Rougeulle
  2. Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7216 Epigenetics and Cell Fate, Paris, France
    Céline Vallot, Christophe Huret & Claire Rougeulle
  3. Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon 1, Villeurbanne, France
    Yann Lesecque & Laurent Duret
  4. Stem Cell Institute, University of Connecticut Health Center, Farmington, Connecticut, USA
    Alissa Resch
  5. ESTeam Paris Sud, Institut National de la Santé et de la Recherche Médicale (INSERM) U935, Université Paris Sud 11, Assistance Publique–Hôpitaux de Paris (AP-HP), Villejuif, France
    Noufissa Oudrhiri & Annelise Bennaceur-Griscelli

Authors

  1. Céline Vallot
  2. Christophe Huret
  3. Yann Lesecque
  4. Alissa Resch
  5. Noufissa Oudrhiri
  6. Annelise Bennaceur-Griscelli
  7. Laurent Duret
  8. Claire Rougeulle

Contributions

C.V. and C.H. performed the experiments. Y.L. and L.D. did the bioinformatic analysis of XACT conservation. N.O. and A.B.-G. provided the H9-MSC-iPS system. A.R. contributed to the bioinformatics analysis of the RNA-seq data. C.V. and C.R. conceived and designed the experiments, and wrote the manuscript.

Corresponding author

Correspondence toClaire Rougeulle.

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The authors declare no competing financial interests.

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Vallot, C., Huret, C., Lesecque, Y. et al. XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells.Nat Genet 45, 239–241 (2013). https://doi.org/10.1038/ng.2530

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