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.

  • Letter
  • Published:

Regulation of cell cycle progression and gene expression by H2A deubiquitination

Nature volume 449, pages 1068–1072 (2007)Cite this article

Abstract

Post-translational histone modifications have important regulatory roles in chromatin structure and function1,2,3. One example of such modifications is histone ubiquitination, which occurs predominately on histone H2A and H2B. Although the recent identification of the ubiquitin ligase for histone H2A has revealed important roles for H2A ubiquitination in Hox gene silencing4,5,6 as well as in X-chromosome inactivation7,8, the enzyme(s) involved in H2A deubiquitination and the function of H2A deubiquitination are not known. Here we report the identification and functional characterization of the major deubiquitinase for histone H2A, Ubp-M (also called USP16). Ubp-M prefers nucleosomal substrates in vitro, and specifically deubiquitinates histone H2A but not H2B in vitro and in vivo. Notably, knockdown of Ubp-M in HeLa cells results in slow cell growth rates owing to defects in the mitotic phase of the cell cycle. Further studies reveal that H2A deubiquitination by Ubp-M is a prerequisite for subsequent phosphorylation of Ser 10 of H3 and chromosome segregation when cells enter mitosis. Furthermore, we demonstrate that Ubp-M regulates Hox gene expression through H2A deubiquitination and that blocking the function of Ubp-M results in defective posterior development in Xenopus laevis. This study identifies the major deubiquitinase for histone H2A and demonstrates that H2A deubiquitination is critically involved in cell cycle progression and gene expression.

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

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

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

Figure 1: Purification of the H2A-specific deubiquitinase.
Figure 2: Substrate preference and specificity of Ubp-M.
Figure 3: Ubp-M-mediated H2A deubiquitination is required for cell cycle M phase progression.
Figure 4: Ubp-M-mediated H2A deubiquitination regulates Hox gene expression.

Similar content being viewed by others

References

  1. Martin, C. & Zhang, Y. The diverse functions of histone lysine methylation. Nature Rev. Mol. Cell Biol. 6, 838–849 (2005)

    Article  CAS  Google Scholar 

  2. Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074–1080 (2001)

    Article  CAS  Google Scholar 

  3. Peterson, C. L. & Laniel, M.-A. Histones and histone modifications. Curr. Biol. 14, R546–R551 (2004)

    Article  CAS  Google Scholar 

  4. Wang, H. et al. Role of histone H2A ubiquitination in Polycomb silencing. Nature 431, 873–878 (2004)

    Article  ADS  CAS  Google Scholar 

  5. Cao, R., Tsukada, Y.-i. & Zhang, Y. Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. Mol. Cell 20, 845–854 (2005)

    Article  CAS  Google Scholar 

  6. Wei, J., Zhai, L., Xu, J. & Wang, H. Role of Bmi1 in H2A ubiquitylation and Hox gene silencing. J. Biol. Chem. 281, 22537–22544 (2006)

    Article  CAS  Google Scholar 

  7. Fang, J., Chen, T., Chadwick, B., Li, E. & Zhang, Y. Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation. J. Biol. Chem. 279, 52812–52815 (2004)

    Article  CAS  Google Scholar 

  8. de Napoles, M. et al. Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Dev. Cell 7, 663–676 (2004)

    Article  CAS  Google Scholar 

  9. Fang, J., Wang, H. & Zhang, Y. Purification of histone methyltransferases from HeLa cells. Methods Enzymol. 377, 213–226 (2004)

    Article  CAS  Google Scholar 

  10. Wang, H. et al. Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase. Mol. Cell 8, 1207–1217 (2001)

    Article  CAS  Google Scholar 

  11. Henry, K. W. et al. Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 17, 2648–2663 (2003)

    Article  CAS  Google Scholar 

  12. Daniel, J. A. et al. Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J. Biol. Chem. 279, 1867–1871 (2004)

    Article  CAS  Google Scholar 

  13. Erdjument-Bromage, H. et al. Examination of micro-tip reversed-phase liquid chromatographic extraction of peptide pools for mass spectrometric analysis. J. Chromatogr. A. 826, 167–181 (1988)

    Article  Google Scholar 

  14. Winkler, G. et al. Isolation and mass spectrometry of transcription factor complexes. Methods 26, 260–269 (2002)

    Article  CAS  Google Scholar 

  15. Cai, S. Y., Babbitt, R. & Marchesi, V. A mutant deubiquitinating enzyme (Ubp-M) associates with mitotic chromosomes and blocks cell division. Proc. Natl Acad. Sci. USA 96, 2828–2833 (1999)

    Article  ADS  CAS  Google Scholar 

  16. Mimnaugh, E. G. et al. Caspase-dependent deubiquitination of monoubiquitinated nucleosomal histone H2A induced by diverse apoptogenic stimuli. Cell Death Differ. 8, 1182–1196 (2001)

    Article  CAS  Google Scholar 

  17. Wang, H. et al. Histone H3 and H4 ubiquitylation by the CUL4-DDB-ROC1 ubiquitin ligase facilitates cellular response to DNA damage. Mol. Cell 22, 383–394 (2006)

    Article  Google Scholar 

  18. Shiio, Y. & Eisenman, R. N. Histone sumoylation is associated with transcriptional repression. Proc. Natl Acad. Sci. USA 100, 13225–13230 (2003)

    Article  ADS  CAS  Google Scholar 

  19. Robzyk, K., Recht, J. & Osley, M. A. Rad6-dependent ubiquitination of histone H2B in yeast. Science 287, 501–504 (2000)

    Article  ADS  CAS  Google Scholar 

  20. Henry, K. W. et al. Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 17, 2648–2663 (2003)

    Article  CAS  Google Scholar 

  21. Emre, N. C. T. et al. Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal sir2 association and gene silencing. Mol. Cell 17, 585–594 (2005)

    Article  CAS  Google Scholar 

  22. Luger, K., Rechsteiner, T. J. & Richmond, T. J. Preparation of nucleosome core particle from recombinant histones. Methods Enzymol. 304, 3–19 (1999)

    Article  CAS  Google Scholar 

  23. Dyer, P. N. et al. Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol. 375, 23–44 (2004)

    Article  CAS  Google Scholar 

  24. Dignam, J. D., Martin, P., Shastry, B. & Roeder, R. Eukaryotic gene transcription with purified components. Methods Enzymol. 101, 582–598 (1983)

    Article  CAS  Google Scholar 

  25. Fischle, W. et al. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438, 1116–1122 (2005)

    Article  ADS  CAS  Google Scholar 

  26. Harland, R. M. In situ hybridization: an improved whole-mount method for Xenopus embryos. Methods Cell Biol. 36, 685–695 (1991)

    Article  CAS  Google Scholar 

  27. Bolton, M. A. et al. Aurora B kinase exists in a complex with survivin and INCENP and its kinase activity is stimulated by survivin binding and phosphorylation. Mol. Biol. Cell 13, 3064–3077 (2002)

    Article  CAS  Google Scholar 

  28. Perez-Burgos, L. et al. Generation and characterization of methyl-lysine histone antibodies. Methods Enzymol. 376, 234–254 (2003)

    Article  Google Scholar 

  29. Song, L. et al. Ser-10 phosphorylated histone H3 is involved in cytokinesis as a chromosomal passenger. Cell Biol. Int. 31, 1184–1190 (2007)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

We thank S. L. Berger and M. A. Osley for yeast strains; J. J. Hayes for XP-10 plasmid; and J. Wei for the initial cloning of Ubp-M. We also thank D. Crawford and W. S. Brooks for suggestions on cell cycle and apoptosis analysis; T. Townes and W. S. Brooks for critical reading of the manuscript; E. F. Keyser for assistance with FACS analysis; and A. Nazarian for help with mass spectrometric analysis. This work was supported by a start-up grant (to H.W.) and NCI Cancer Center Support Grant (to P.T.).

Author Contributions H.W. designed the experimental strategy, performed parts of the purification and wrote the paper; H.-Y.J. performed most of the purification, determined the substrate preference and investigated the role of Ubp-M in cell cycle progression and gene expression; L.Z. determined the substrate specificity of Ubp-M and performed the in vitro kinase reaction and nucleosome pull-down experiments; C.Y. cloned the Xenopus Hoxd10 gene and generated the RNAi-resistant Ubp-M constructs; S.N. and C.C. performed the Xenopus injection and in situ hybridization; H.E.-B. and P.T. performed mass spectrometric analysis.

Author information

Author notes

  1. Heui-Yun Joo and Ling Zhai: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Kaul Human Genetics Building 402A, 720 South 20th Street, Birmingham, Alabama 35294, USA,

    Heui-Yun Joo, Ling Zhai, Chunying Yang & Hengbin Wang

  2. Department of Cell Biology, University of Alabama at Birmingham, MCLM 360, Birmingham, Alabama 35294-0005, USA,

    Shuyi Nie & Chenbei Chang

  3. Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA ,

    Hediye Erdjument-Bromage & Paul Tempst

Authors
  1. Heui-Yun Joo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ling Zhai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chunying Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shuyi Nie
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hediye Erdjument-Bromage
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Paul Tempst
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Chenbei Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hengbin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hengbin Wang.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S15 with Legends. (PDF 1263 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Joo, HY., Zhai, L., Yang, C. et al. Regulation of cell cycle progression and gene expression by H2A deubiquitination. Nature 449, 1068–1072 (2007). https://doi.org/10.1038/nature06256

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature06256

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

Advanced 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