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A model for transmission of the H3K27me3 epigenetic mark

An Erratum to this article was published on 01 December 2008

This article has been updated

Abstract

Organization of chromatin by epigenetic mechanisms is essential for establishing and maintaining cellular identity in developing and adult organisms. A key question that remains unresolved about this process is how epigenetic marks are transmitted to the next cell generation during cell division. Here we provide a model to explain how trimethylated Lys 27 of histone 3 (H3K27me3), which is catalysed by the EZH2-containing Polycomb Repressive Complex 2 (PRC2), is maintained in proliferating cells. We show that the PRC2 complex binds to the H3K27me3 mark and colocalizes with this mark in G1 phase and with sites of ongoing DNA replication. Efficient binding requires an intact trimeric PRC2 complex containing EZH2, EED and SUZ12, but is independent of the catalytic SET domain of EZH2. Using a heterologous reporter system, we show that transient recruitment of the PRC2 complex to chromatin, upstream of the transcriptional start site, is sufficient to maintain repression through endogenous PRC2 during subsequent cell divisions. Thus, we suggest that once the H3K27me3 is established, it recruits the PRC2 complex to maintain the mark at sites of DNA replication, leading to methylation of H3K27 on the daughter strands during incorporation of newly synthesized histones. This mechanism ensures maintenance of the H3K27me3 epigenetic mark in proliferating cells, not only during DNA replication when histones synthesized de novo are incorporated, but also outside S phase, thereby preserving chromatin structure and transcriptional programs.

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Figure 1: EZH2 localizes to replication foci and directly interacts with its own methylation site (H3K27me3).
Figure 2: The three PcG proteins of the PRC2 complex are required for binding H3K27me3.
Figure 3: Recruitment of EED to the promoter of a stably integrated reporter leads to transcriptional repression and H3K27 trimethylation.
Figure 4: Transient recruitment of GAL4–EED to the promoter of an integrated reporter is sufficient for maintaining the H3K27me3 mark and transcriptional repression during subsequent cell division cycles.
Figure 5: Endogenous PRC2 is required for maintenance of repression.
Figure 6: Establishment of repression can occur independently of the EZH2 catalytic domain.
Figure 7: Histone H3K27 methylation is required for the maintenance of repression.
Figure 8: Model for maintenance of the H3K27me3 epigenetic mark during cell proliferation.

Change history

  • 28 October 2008

    In the version of this article initially published, the order of the labels siRNA cyclophilin B and siRNA SUZ12 in figure 5 and GAL4-EZH2WT and GAL4-EZH2ΔSET in figure 7a were reversed. The corrected panels are shown below. These errors have also been corrected in the HTML and PDF versions of the article.

References

  1. Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002).

    CAS  Article  PubMed  Google Scholar 

  2. Czermin, B. et al. Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111, 185–196 (2002).

    CAS  Article  PubMed  Google Scholar 

  3. Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16, 2893–2905 (2002).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. Muller, J. et al. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111, 197–208 (2002).

    CAS  Article  PubMed  Google Scholar 

  5. Ebert, A. et al. Su(var) genes regulate the balance between euchromatin and heterochromatin in Drosophila. Genes Dev. 18, 2973–2983 (2004).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. Pasini, D., Bracken, A. P., Hansen, J. B., Capillo, M. & Helin, K. The polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol. Cell Biol. 27, 3769–3779 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. O'Carroll, D. et al. The polycomb-group gene Ezh2 is required for early mouse development. Mol. Cell Biol. 21, 4330–4336 (2001).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. Boyer, L. A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349–353 (2006).

    CAS  Article  PubMed  Google Scholar 

  9. Lee, T. I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. Bracken, A. P., Dietrich, N., Pasini, D., Hansen, K. H. & Helin, K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 20, 1123–1136 (2006).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. Faust, C., Lawson, K. A., Schork, N. J., Thiel, B. & Magnuson, T. The Polycomb-group gene eed is required for normal morphogenetic movements during gastrulation in the mouse embryo. Development 125, 4495–4506 (1998).

    CAS  PubMed  Google Scholar 

  12. Pasini, D., Bracken, A. P., Jensen, M. R., Lazzerini Denchi, E. & Helin, K. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J. 23, 4061–4071 (2004).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. Margueron, R., Trojer, P. & Reinberg, D. The key to development: interpreting the histone code? Curr. Opin. Genet. Dev. 15, 163–176 (2005).

    CAS  Article  PubMed  Google Scholar 

  14. Bird, A. Perceptions of epigenetics. Nature 447, 396–398 (2007).

    CAS  Article  PubMed  Google Scholar 

  15. Ringrose, L. & Paro, R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38, 413–443 (2004).

    CAS  Article  PubMed  Google Scholar 

  16. Sparmann, A. & van Lohuizen, M. Polycomb silencers control cell fate, development and cancer. Nature Rev. Cancer 6, 846–856 (2006).

    CAS  Article  Google Scholar 

  17. Valk-Lingbeek, M. E., Bruggeman, S. W. & van Lohuizen, M. Stem cells and cancer; the polycomb connection. Cell 118, 409–418 (2004).

    CAS  Article  PubMed  Google Scholar 

  18. Muller, H. et al. E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis. Genes Dev. 15, 267–285 (2001).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. Bracken, A. P. et al. EZH2 is downstream of the pRB–E2F pathway, essential for proliferation and amplified in cancer. EMBO J. 22, 5323–5335 (2003).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. Moldovan, G. L., Pfander, B. & Jentsch, S. PCNA, the maestro of the replication fork. Cell 129, 665–679 (2007).

    CAS  Article  PubMed  Google Scholar 

  21. Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410, 116–120 (2001).

    CAS  Article  PubMed  Google Scholar 

  22. Bannister, A. J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001).

    CAS  Article  PubMed  Google Scholar 

  23. Lai, J. S. & Herr, W. Ethidium bromide provides a simple tool for identifying genuine DNA-independent protein associations. Proc. Natl Acad. Sci. USA 89, 6958–6962 (1992).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. van Lohuizen, M. et al. Interaction of mouse polycomb-group (Pc-G) proteins Enx1 and Enx2 with Eed: indication for separate Pc-G complexes. Mol. Cell Biol. 18, 3572–3579 (1998).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. Reinberg, D & Sims RJ. de FACTo nuclear dynamics. J. Biol. Chem. 281, 23297–23301 (2006).

    CAS  Article  PubMed  Google Scholar 

  26. Dietrich, N et al. Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A–ARF locus. EMBO J. (2007).

  27. Muller, J. & Kassis, J. A. Polycomb response elements and targeting of Polycomb group proteins in Drosophila. Curr. Opin. Genet. Dev. 16, 476–484 (2006).

    Article  PubMed  Google Scholar 

  28. Schwartz, Y. B. & Pirrotta, V. Polycomb silencing mechanisms and the management of genomic programmes. Nature Rev. Genet. 8, 9–22 (2007).

    CAS  Article  PubMed  Google Scholar 

  29. Brown, J. L., Mucci, D., Whiteley, M., Dirksen, M. L. & Kassis, J. A. The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1. Mol. Cell 1, 1057–1064 (1998).

    CAS  Article  PubMed  Google Scholar 

  30. Brown, J. L., Fritsch, C., Mueller, J. & Kassis, J. A. The Drosophila pho-like gene encodes a YY1-related DNA binding protein that is redundant with pleiohomeotic in homeotic gene silencing. Development 130, 285–94 (2003).

    CAS  Article  PubMed  Google Scholar 

  31. Negre, N. et al. Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol. 4, e170 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  32. Squazzo, S. L. et al. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res. 16, 890–900 (2006).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007).

    CAS  Article  PubMed  Google Scholar 

  34. Poux, S., Melfi, R. & Pirrotta, V. Establishment of Polycomb silencing requires a transient interaction between PC and ESC. Genes Dev. 15, 2509–2514 (2001).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  35. Shao, Z. et al. Stabilization of chromatin structure by PRC1, a Polycomb complex. Cell 98, 37–46 (1999).

    CAS  Article  PubMed  Google Scholar 

  36. Francis, N. J., Saurin, A. J., Shao, Z. & Kingston, R. E. Reconstitution of a functional core polycomb repressive complex. Mol. Cell 8, 545–556 (2001).

    CAS  Article  PubMed  Google Scholar 

  37. McCall, K. & Bender, W. Probes of chromatin accessibility in the Drosophila bithorax complex respond differently to Polycomb-mediated repression. EMBO J. 15, 569–580 (1996).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  38. Levine, S. S., King, I. F. & Kingston, R. E. Division of labor in polycomb group repression. Trends Biochem. Sci. 29, 478–485 (2004).

    CAS  Article  PubMed  Google Scholar 

  39. Hernandez-Munoz, I., Taghavi, P., Kuijl, C., Neefjes, J. & van Lohuizen, M. Association of BMI1 with polycomb bodies is dynamic and requires PRC2/EZH2 and the maintenance DNA methyltransferase DNMT1. Mol. Cell Biol. 25, 11047–11058 (2005).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  40. Agger, K. et al. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449, 731–734 (2007).

    CAS  Article  PubMed  Google Scholar 

  41. De Santa, F. et al. The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. Cell 130, 1083–1094 (2007).

    CAS  Article  PubMed  Google Scholar 

  42. Hong, S. et al. Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. Proc. Natl Acad. Sci. USA 104, 18439–18444 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  43. Lan, F. et al. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449, 689–694 (2007).

    CAS  Article  PubMed  Google Scholar 

  44. Lee, M. G. et al. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science 318, 447–450 (2007).

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

We thank Danny Reinberg for providing the 5×Gal4TKLucNeo reporter plasmid. We thank members of the Helin laboratory for technical advice and fruitful discussion. This work was supported by grants from the Novo Nordisk Foundation, Association for International Cancer Research, the Danish Cancer Society, the Danish Medical Research Council, the Danish Natural Science Research Council and the Danish National Research Foundation.

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Authors and Affiliations

Authors

Contributions

K.H.H. performed most of the experiments; A.P.B. performed ChIP analysis including qPCR on material provided by K.H.H., except for the experiment in Fig. 6c, which was performed by S.S.G.; DP made the ΔSANT2 mutant of EZH2; N.D. helped to establish the Gal4EZH2WT and ΔSET reporter cell lines; A.M. cloned the shRNA construct for Gal4; J.R. performed the final mass spectrometry analysis on samples provided by K.H.H.; ML performed the confocal microscopy analysis on cell stainings provided by K.H.H.; K.H.H. and K.H. jointly conceived the project and wrote the manuscript.

Corresponding authors

Correspondence to Klaus H. Hansen or Kristian Helin.

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Hansen, K., Bracken, A., Pasini, D. et al. A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol 10, 1291–1300 (2008). https://doi.org/10.1038/ncb1787

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