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XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells

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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Figure 1: Characterization of XACT, a long intergenic RNA that coats the active X chromosome in hESCs.
Figure 2: XACT coats both X chromosomes in hESCs not expressing XIST, and the expression of XACT is restricted to pluripotent cells.

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Gene Expression Omnibus

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 

Download references

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

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  1. Céline Vallot
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  8. Claire Rougeulle
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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 to Claire 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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