Skip to main content

Thank you for visiting nature.com. 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.

RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation

Abstract

Evolution of the mammalian sex chromosomes has resulted in a heterologous X and Y pair, where the Y chromosome has lost most of its genes. Hence, there is a need for X-linked gene dosage compensation between XY males and XX females. In placental mammals, this is achieved by random inactivation of one X chromosome in all female somatic cells1. Upregulation of Xist transcription on the future inactive X chromosome acts against Tsix antisense transcription, and spreading of Xist RNA in cis triggers epigenetic changes leading to X-chromosome inactivation. Previously, we have shown that the X-encoded E3 ubiquitin ligase RNF12 is upregulated in differentiating mouse embryonic stem cells and activates Xist transcription and X-chromosome inactivation2. Here we identify the pluripotency factor REX1 as a key target of RNF12 in the mechanism of X-chromosome inactivation. RNF12 causes ubiquitination and proteasomal degradation of REX1, and Rnf12 knockout embryonic stem cells show an increased level of REX1. Using chromatin immunoprecipitation sequencing, REX1 binding sites were detected in Xist and Tsix regulatory regions. Overexpression of REX1 in female embryonic stem cells was found to inhibit Xist transcription and X-chromosome inactivation, whereas male Rex1+/− embryonic stem cells showed ectopic X-chromosome inactivation. From this, we propose that RNF12 causes REX1 breakdown through dose-dependent catalysis, thereby representing an important pathway to initiate X-chromosome inactivation. Rex1 and Xist are present only in placental mammals, which points to co-evolution of these two genes and X-chromosome inactivation.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Figure 1: RNF12 interacts with REX1 in mouse ESCs.
Figure 2: RNF12 polyubiquitinates and targets REX1 for proteasomal degradation.
Figure 3: RNF12 is a dose-dependent regulator of REX1 expression.
Figure 4: REX1-dependent regulation of XCI.

References

  1. Lyon, M. F. Gene action in the X-chromosome of the mouse (Mus musculus L.). Nature 190, 372–373 (1961)

    Article  ADS  CAS  Google Scholar 

  2. Jonkers, I. et al. RNF12 is an X-encoded dose-dependent activator of X chromosome inactivation. Cell 139, 999–1011 (2009)

    Article  CAS  Google Scholar 

  3. Monkhorst, K. et al. The probability to initiate X chromosome inactivation is determined by the X to autosomal ratio and X chromosome specific allelic properties. PLoS ONE 4, e5616 (2009)

    Article  ADS  Google Scholar 

  4. Monkhorst, K., Jonkers, I., Rentmeester, E., Grosveld, F. & Gribnau, J. X inactivation counting and choice is a stochastic process: evidence for involvement of an X-linked activator. Cell 132, 410–421 (2008)

    Article  CAS  Google Scholar 

  5. Shin, J. et al. Maternal Rnf12/RLIM is required for imprinted X-chromosome inactivation in mice. Nature 467, 977–981 (2010)

    Article  ADS  CAS  Google Scholar 

  6. Barakat, T. S. et al. RNF12 activates Xist and is essential for X chromosome inactivation. PLoS Genet. 7, e1002001 (2011)

    Article  CAS  Google Scholar 

  7. Hosler, B. A., LaRosa, G. J., Grippo, J. F. & Gudas, L. J. Expression of REX-1, a gene containing zinc finger motifs, is rapidly reduced by retinoic acid in F9 teratocarcinoma cells. Mol. Cell. Biol. 9, 5623–5629 (1989)

    Article  CAS  Google Scholar 

  8. Scotland, K. B., Chen, S., Sylvester, R. & Gudas, L. J. Analysis of Rex1 (zfp42) function in embryonic stem cell differentiation. Dev. Dyn. 238, 1863–1877 (2009)

    Article  CAS  Google Scholar 

  9. Navarro, P. et al. Molecular coupling of Tsix regulation and pluripotency. Nature 468, 457–460 (2010)

    Article  ADS  CAS  Google Scholar 

  10. Kim, J. D. et al. Rex1/Zfp42 as an epigenetic regulator for genomic imprinting. Hum. Mol. Genet. 20, 1353–1362 (2011)

    Article  CAS  Google Scholar 

  11. Masui, S. et al. Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells. BMC Dev. Biol. 8, 45 (2008)

    Article  Google Scholar 

  12. Kim, J. D., Faulk, C. & Kim, J. Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1. Nucleic Acids Res. 35, 3442–3452 (2007)

    Article  CAS  Google Scholar 

  13. Donohoe, M. E. et al. Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch. Mol. Cell 25, 43–56 (2007)

    Article  CAS  Google Scholar 

  14. Duret, L. et al. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 312, 1653–1655 (2006)

    Article  ADS  CAS  Google Scholar 

  15. van den Berg, D. L. et al. An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 6, 369–381 (2010)

    Article  CAS  Google Scholar 

  16. Soler, E. et al. A systems approach to analyze transcription factors in mammalian cells. Methods 53, 151–162 (2011)

    Article  CAS  Google Scholar 

  17. Dignam, J. D., Lebovitz, R. M. & Roeder, R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11, 1475–1489 (1983)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank R. van der Linden and C. Maduro for their help with some of the experiments, A. Inagaki, C. Andrieu-Soler, D. Warmerdam, L. Zhang and A. Mohd-Sarip for experimental advice, and C. Rougeulle and R. Jaenisch for providing the Tsix-stop cells. This work was supported by grants from the Netherlands Organisation for Scientific Research (NWO-TOP and NWO-VICI) and the European Research Council to J.G.

Author information

Authors and Affiliations

Authors

Contributions

C.G. and J.G. designed the experiments. C.G. performed most experiments assisted by E.R. T.S.B., C.G. and J.G. generated the Rnf12−/− ES cells line. C.G., J.D., W.v.IJ. and E.M.A. performed the mass spectrometry and sequencing analysis. J.G., J.A.G. and C.G. wrote the manuscript.

Corresponding author

Correspondence to Joost Gribnau.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-10 and Supplementary Tables 1-3. (PDF 1482 kb)

Supplementary Tables

This file contains Supplementary Table 4. (XLS 2610 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gontan, C., Achame, E., Demmers, J. et al. RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation. Nature 485, 386–390 (2012). https://doi.org/10.1038/nature11070

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature11070

This article is cited by

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.

Search

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