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.

  • Article
  • Published:

H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system

Nature Plants volume 2, Article number: 16126 (2016) Cite this article

Subjects

Abstract

Polycomb group (PcG) proteins form an epigenetic memory system in plants and animals, but interacting proteins are poorly known in plants. Here, we have identified Arabidopsis UBIQUITIN SPECIFIC PROTEASES (USP; UBP in plant and yeasts) 12 and 13 as partners of the plant-specific PcG protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1). UBP12 binds to chromatin of PcG target genes and is required for histone H3 lysine 27 trimethylation and repression of a subset of PcG target genes. Plants lacking UBP12 and UBP13 developed autonomous endosperm in the absence of fertilization. We have identified UBP12 and UBP13 as new proteins in the plant PcG regulatory network. UBP12 and UBP13 belong to an ancient gene family and represent plant homologues of metazoan USP7. We have found that Drosophila USP7 shares a function in heterochromatic gene repression with UBP12/13 and their homologue UBP26. In summary, we demonstrate that USP7-like proteins are essential for gene silencing in diverse genomic contexts.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: UBP12 and UBP13 interact with LHP1 in vivo.
Figure 2: UBP12 and UBP13 are required for repression of PcG protein targets.
Figure 3: UBP12 binds to PcG target chromatin and H3K27me3 is locally reduced in ubp13-2 ubp12-1+/– plants.
Figure 4: UBP12 and UBP13 prevent autonomous endosperm development.
Figure 5: UBP12 is an H2Aub deubiquitinase.
Figure 6: Drosophila USP7 is required for heterochromatin formation and transposon repression.

Similar content being viewed by others

References

  1. Lewis, E. B. A gene complex controlling segmentation in Drosophila. Nature 276, 565–570 (1978).

    Article  CAS  Google Scholar 

  2. Simon, J. A. & Kingston, R. E. Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol. Cell 49, 808–824 (2013).

    Article  CAS  Google Scholar 

  3. Derkacheva, M. & Hennig, L. Variations on a theme: Polycomb group proteins in plants. J. Exp. Bot. 65, 2769–2784 (2014).

    Article  CAS  Google Scholar 

  4. Holec, S. & Berger, F. Polycomb group complexes mediate developmental transitions in plants. Plant Physiol. 158, 35–43 (2012).

    Article  CAS  Google Scholar 

  5. Bratzel, F., Lopez-Torrejon, G., Koch, M., Del Pozo, J. C. & Calonje, M. Keeping cell identity in Arabidopsis requires PRC1 RING-finger homologs that catalyze H2A monoubiquitination. Curr. Biol. 20, 1853–1859 (2010).

    Article  CAS  Google Scholar 

  6. Yang, C. et al. VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis. Curr. Biol. 23, 1324–1329 (2013).

    Article  CAS  Google Scholar 

  7. Blackledge, N. P. et al. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell 157, 1445–1459 (2014).

    Article  CAS  Google Scholar 

  8. Calonje, M. PRC1 marks the difference in plant PcG repression. Mol. Plant 7, 459–471 (2014).

    Article  CAS  Google Scholar 

  9. Cooper, S. et al. Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment. Cell Rep. 7, 1456–1470 (2014).

    Article  CAS  Google Scholar 

  10. Kalb, R. et al. Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression. Nat. Struct. Mol. Biol. 21, 569–571 (2014).

    Article  CAS  Google Scholar 

  11. Sanchez-Pulido, L., Devos, D., Sung, Z. R. & Calonje, M. RAWUL: a new Ubiquitin-like domain in PRC1 Ring finger proteins that unveils putative plant and worm PRC1 orthologs. BMC Genomics 9, 308 (2008).

    Article  Google Scholar 

  12. Xu, L. & Shen, W. H. Polycomb silencing of KNOX genes confines shoot stem cell niches in Arabidopsis. Curr. Biol. 18, 1966–1971 (2008).

    Article  CAS  Google Scholar 

  13. Turck, F. et al. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of Histone H3 Lysine 27. PLoS Genet. 3, 0855–0866 (2007).

    Article  CAS  Google Scholar 

  14. Zhang, X. et al. The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat. Struct. Mol. Biol. 14, 869–871 (2007).

    Article  CAS  Google Scholar 

  15. Exner, V. et al. The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development. PLoS ONE 4, e5335 (2009).

    Article  Google Scholar 

  16. Kotake, T., Takada, S., Nakahigashi, K., Ohto, M. & Goto, K. Arabidopsis TERMINAL FLOWER 2 gene encodes a LIKE HETEROCHROMATIN PROTEIN 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes. Plant Cell Physiol. 44, 555–564 (2003).

    Article  CAS  Google Scholar 

  17. Libault, M. et al. The Arabidopsis LHP1 protein is a component of euchromatin. Planta 222, 910–925 (2005).

    Article  CAS  Google Scholar 

  18. Derkacheva, M. et al. Arabidopsis MSI1 connects LHP1 to PRC2 complexes. EMBO J. 32, 2073–2085 (2013).

    Article  CAS  Google Scholar 

  19. Wang, Y., Gu, X., Yuan, W., Schmitz, R. J. & He, Y. Photoperiodic control of the floral transition through a distinct polycomb repressive complex. Dev. Cell 28, 727–736 (2014).

    Article  CAS  Google Scholar 

  20. Makarova, K. S., Aravind, L. & Koonin, E. V. A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae. Trends Biochem. Sci. 25, 50–52 (2000).

    Article  CAS  Google Scholar 

  21. Yan, N., Doelling, J. H., Falbel, T. G., Durski, A. M. & Vierstra, R. D. The ubiquitin-specific protease family from Arabidopsis. AtUBP1 and 2 are required for the resistance to the amino acid analog canavanine. Plant Physiol 124, 1828–1843 (2000).

    Article  CAS  Google Scholar 

  22. Liu, Y. et al. Functional characterization of the Arabidopsis ubiquitin-specific protease gene family reveals specific role and redundancy of individual members in development. Plant J. 55, 844–856 (2008).

    Article  CAS  Google Scholar 

  23. Ewan, R. et al. Deubiquitinating enzymes AtUBP12 and AtUBP13 and their tobacco homologue NtUBP12 are negative regulators of plant immunity. New Phytol. 191, 92–106 (2011).

    Article  CAS  Google Scholar 

  24. Doelling, J. H. et al. The ubiquitin-specific protease subfamily UBP3/UBP4 is essential for pollen development and transmission in Arabidopsis. Plant Physiol. 145, 801–813 (2007).

    Article  CAS  Google Scholar 

  25. Sridhar, V. V. et al. Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature 447, 735–738 (2007).

    Article  CAS  Google Scholar 

  26. Cui, X. et al. Ubiquitin-specific proteases UBP12 and UBP13 act in circadian clock and photoperiodic flowering regulation in Arabidopsis. Plant Physiol. 162, 897–906 (2013).

    Article  CAS  Google Scholar 

  27. Shen, L. et al. The putative PRC1 RING-finger protein AtRING1A regulates flowering through repressing MADS AFFECTING FLOWERING genes in Arabidopsis. Development 141, 1303–1312 (2014).

    Article  CAS  Google Scholar 

  28. Ohad, N. et al. A mutation that allows endosperm development without fertilization. Proc. Natl Acad. Sci. USA 93, 5319–5324 (1996).

    Article  CAS  Google Scholar 

  29. Chaudhury, A. M. et al. Fertilization-independent seed development in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 94, 4223–4228 (1997).

    Article  CAS  Google Scholar 

  30. Köhler, C. et al. Arabidopsis MSI1 is a component of the MEA/FIE Polycomb group complex and required for seed development. EMBO J. 22, 4804–4814 (2003).

    Article  Google Scholar 

  31. Guitton, A. E. et al. Identification of new members of FERTILISATION INDEPENDENT SEED Polycomb group pathway involved in the control of seed development in Arabidopsis thaliana. Development 131, 2971–2981 (2004).

    Article  CAS  Google Scholar 

  32. Pillot, M. et al. Embryo and endosperm inherit distinct chromatin and transcriptional states from the female gametes in Arabidopsis. Plant Cell 22, 307–320 (2010).

    Article  CAS  Google Scholar 

  33. Wuest, S. E. et al. Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes. Curr. Biol. 20, 506–512 (2010).

    Article  CAS  Google Scholar 

  34. Roszak, P. & Köhler, C. Polycomb group proteins are required to couple seed coat initiation to fertilization. Proc. Natl Acad. Sci USA 108, 20826–20831 (2011).

    Article  CAS  Google Scholar 

  35. Mozgova, I. & Hennig, L. The polycomb group protein regulatory network. Annu. Rev. Plant Biol. 66, 269–296 (2015).

    Article  CAS  Google Scholar 

  36. Scheuermann, J. C. et al. Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature 465, 243–247 (2010).

    Article  CAS  Google Scholar 

  37. Cotto-Rios, X. M., Bekes, M., Chapman, J., Ueberheide, B. & Huang, T. T. Deubiquitinases as a signaling target of oxidative stress. Cell Rep. 2, 1475–1484 (2012).

    Article  CAS  Google Scholar 

  38. Lee, J. G., Baek, K., Soetandyo, N. & Ye, Y. Reversible inactivation of deubiquitinases by reactive oxygen species in vitro and in cells. Nat. Commun. 4, 1568 (2013).

    Article  Google Scholar 

  39. Luo, M. et al. UBIQUITIN-SPECIFIC PROTEASE 26 is required for seed development and the repression of PHERES1 in Arabidopsis. Genetics 180, 229–236 (2008).

    Article  CAS  Google Scholar 

  40. Schmitz, R. J., Tamada, Y., Doyle, M. R., Zhang, X. & Amasino, R. M. Histone H2B deubiquitination is required for transcriptional activation of FLOWERING LOCUS C and for proper control of flowering in Arabidopsis. Plant Physiol. 149, 1196–1204 (2009).

    Article  CAS  Google Scholar 

  41. van der Knaap, J. A. et al. GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7. Mol. Cell 17, 695–707 (2005).

    Article  CAS  Google Scholar 

  42. Tartof, K. D., Hobbs, C. & Jones, M. A structural basis for variegating position effects. Cell 37, 869–878 (1984).

    Article  CAS  Google Scholar 

  43. van der Knaap, J. A., Kozhevnikova, E., Langenberg, K., Moshkin, Y. M. & Verrijzer, C. P. Biosynthetic enzyme GMP synthetase cooperates with ubiquitin-specific protease 7 in transcriptional regulation of ecdysteroid target genes. Mol. Cell Biol. 30, 736–744 (2010).

    Article  CAS  Google Scholar 

  44. Gaudin, V. et al. Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. Development 128, 4847–4858 (2001).

    CAS  PubMed  Google Scholar 

  45. Cui, H. & Benfey, P. N. Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root. Plant J. 58, 1016–1027 (2009).

    Article  CAS  Google Scholar 

  46. Liu, C., Xi, W., Shen, L., Tan, C. & Yu, H. Regulation of floral patterning by flowering time genes. Dev. Cell 16, 711–722 (2009).

    Article  CAS  Google Scholar 

  47. Latrasse, D. et al. Control of flowering and cell fate by LIF2, an RNA binding partner of the Polycomb complex component LHP1. PLoS One 6, e16592 (2011).

    Article  CAS  Google Scholar 

  48. Takada, S. & Goto, K. TERMINAL FLOWER 2, an Arabidopsis homolog of HETEROCHROMATIN PROTEIN 1, counteracts the activation of FLOWERING LOCUS T by CONSTANS in the vascular tissues of leaves to regulate flowering time. Plant Cell 15, 2856–2865 (2003).

    Article  CAS  Google Scholar 

  49. Mylne, J. S. et al. LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC. Proc. Natl Acad. Sci. USA 103, 5012–5017 (2006).

    Article  CAS  Google Scholar 

  50. Pengelly, A. R., Kalb, R., Finkl, K. & Muller, J. Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation. Genes Dev. 29, 1487–1492 (2015).

    Article  CAS  Google Scholar 

  51. Scheuermann, J. C., Gutierrez, L. & Muller, J. Histone H2A monoubiquitination and Polycomb repression: the missing pieces of the puzzle. Fly 6, 162–168 (2012).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank B. Liu (Uppsala) for help with protein expression, E. Savenkov (Uppsala) for providing plasmid pSITE–nYFP-N1-2b, M. Blatt (University of Glasgow) for providing a set of ubiquitin promoter-based vectors with fluorescent tags, X. Cui (Chinese Academy of Science, Beijing) for ubp12-2w ubp13-3 seeds and P. Verrijzer (Erasmus University Medical Centre, Rotterdam) for USP7 mutant flies. We thank TAIR and ABRC for mutant seeds and clones. We thank W. Gruissem for continuous support and providing access to infrastructure. This work was supported by grants from ETH Zurich, the Swedish Research Council and the Knut-and-Alice-Wallenberg Foundation.

Author information

Author notes

  1. Maria Derkacheva and Shujing Liu: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden

    Maria Derkacheva, Shujing Liu, Duarte D. Figueiredo, Matthew Gentry, Iva Mozgova, Claudia Köhler & Lars Hennig

  2. Department of Biology and Zurich-Basel Plant Science Centre, ETH Zurich, CH-8092, Zurich, Switzerland

    Maria Derkacheva

  3. Functional Genomics Centre Zurich, University of Zurich/ETH Zürich, CH-8057 Zurich, Switzerland

    Paolo Nanni

  4. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden

    Min Tang & Mattias Mannervik

Authors
  1. Maria Derkacheva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shujing Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Duarte D. Figueiredo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Matthew Gentry
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Iva Mozgova
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Paolo Nanni
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Min Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Mattias Mannervik
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Claudia Köhler
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Lars Hennig
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

M.D., S.L., D.D.F., M.G., I.M., P.N. and M.T. performed the experiments; M.D., S.L., D.D.F., I.M. and P.N. analysed data; M.D., S.L., M.M., C.K. and L.H. planned the experiments; and M.D., M.M., C.K. and L.H. wrote the manuscript.

Corresponding author

Correspondence to Lars Hennig.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Methods, Supplementary Figures, Supplementary Tables 1- 3, Supplementary References (PDF 1122 kb)

Supplementary Information

Supplementary Table 4 (XLSX 25 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Derkacheva, M., Liu, S., Figueiredo, D. et al. H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system. Nature Plants 2, 16126 (2016). https://doi.org/10.1038/nplants.2016.126

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/nplants.2016.126

This article is cited by

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