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Polycomb complexes repress developmental regulators in murine embryonic stem cells


The mechanisms by which embryonic stem (ES) cells self-renew while maintaining the ability to differentiate into virtually all adult cell types are not well understood. Polycomb group (PcG) proteins are transcriptional repressors that help to maintain cellular identity during metazoan development by epigenetic modification of chromatin structure1. PcG proteins have essential roles in early embryonic development2,3,4,5,6 and have been implicated in ES cell pluripotency2, but few of their target genes are known in mammals. Here we show that PcG proteins directly repress a large cohort of developmental regulators in murine ES cells, the expression of which would otherwise promote differentiation. Using genome-wide location analysis in murine ES cells, we found that the Polycomb repressive complexes PRC1 and PRC2 co-occupied 512 genes, many of which encode transcription factors with important roles in development. All of the co-occupied genes contained modified nucleosomes (trimethylated Lys 27 on histone H3). Consistent with a causal role in gene silencing in ES cells, PcG target genes were de-repressed in cells deficient for the PRC2 component Eed, and were preferentially activated on induction of differentiation. Our results indicate that dynamic repression of developmental pathways by Polycomb complexes may be required for maintaining ES cell pluripotency and plasticity during embryonic development.

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Figure 1: PRC1 and PRC2 colocalize at genes encoding developmental regulators.
Figure 2: De-repression of PcG target genes and loss of PRC1 binding in the absence of the PRC2 component Eed.
Figure 3: PcG target genes are preferentially upregulated during ES cell differentiation.


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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  3. 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)

    Article  CAS  Google Scholar 

  4. Shumacher, A., Faust, C. & Magnuson, T. Positional cloning of a global regulator of anterior–posterior patterning in mice. Nature 383, 250–253 (1996)

    Article  ADS  CAS  Google Scholar 

  5. Voncken, J. W. et al. Rnf2 (Ring1b) deficiency causes gastrulation arrest and cell cycle inhibition. Proc. Natl Acad. Sci. USA 100, 2468–2473 (2003)

    Article  ADS  CAS  Google Scholar 

  6. Isono, K. et al. Mammalian polyhomeotic homologues Phc2 and Phc1 act in synergy to mediate polycomb repression of Hox genes. Mol. Cell. Biol. 25, 6694–6706 (2005)

    Article  CAS  Google Scholar 

  7. Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  9. 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)

    Article  CAS  Google Scholar 

  10. 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)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  12. Kirmizis, A. et al. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev. 18, 1592–1605 (2004)

    Article  CAS  Google Scholar 

  13. Hombria, J. C. & Lovegrove, B. Beyond homeosis—HOX function in morphogenesis and organogenesis. Differentiation 71, 461–476 (2003)

    Article  Google Scholar 

  14. Schepers, G. E., Teasdale, R. D. & Koopman, P. Twenty pairs of sox: extent, homology, and nomenclature of the mouse and human sox transcription factor gene families. Dev. Cell 3, 167–170 (2002)

    Article  CAS  Google Scholar 

  15. Lehmann, O. J., Sowden, J. C., Carlsson, P., Jordan, T. & Bhattacharya, S. S. Fox's in development and disease. Trends Genet. 19, 339–344 (2003)

    Article  CAS  Google Scholar 

  16. Showell, C., Binder, O. & Conlon, F. L. T-box genes in early embryogenesis. Dev. Dyn. 229, 201–218 (2004)

    Article  CAS  Google Scholar 

  17. Burch, J. B. Regulation of GATA gene expression during vertebrate development. Semin. Cell Dev. Biol. 16, 71–81 (2005)

    Article  CAS  Google Scholar 

  18. Montgomery, N. D. et al. The murine polycomb group protein Eed is required for global histone H3 lysine-27 methylation. Curr. Biol. 15, 942–947 (2005)

    Article  CAS  Google Scholar 

  19. Cao, R., Tsukada, Y. & 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 

  20. Gidekel, S. & Bergman, Y. A unique developmental pattern of Oct-3/4 DNA methylation is controlled by a cis-demodification element. J. Biol. Chem. 277, 34521–34530 (2002)

    Article  CAS  Google Scholar 

  21. Hattori, N. et al. Epigenetic control of mouse Oct-4 gene expression in embryonic stem cells and trophoblast stem cells. J. Biol. Chem. 279, 17063–17069 (2004)

    Article  CAS  Google Scholar 

  22. Feldman, N. et al. G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nature Cell Biol. 8, 188–194 (2006)

    Article  CAS  Google Scholar 

  23. Vire, E. et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871–874 (2006)

    Article  ADS  CAS  Google Scholar 

  24. Meissner, A. et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33, 5868–5877 (2005)

    Article  CAS  Google Scholar 

  25. Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992)

    Article  CAS  Google Scholar 

  26. Lee, T. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 1–13 (2006)

    Article  Google Scholar 

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We thank Biology and Research Computing (BaRC), especially B. Yuan, T. Dicesare and T. Volkert, at the Whitehead Institute's Center for Microarray Technology, as well as E. Herbolsheimer, for computational and technical support. We also thank members of the Gifford, Young and Jaenisch laboratories for discussions and critical review of the manuscript. We are grateful to T. Magnuson for the Eed mutant (17Rn5-3354SB) ES cell lines. L.A.B. was supported in part by an NIH NRSA fellowship. K.P. is a special fellow of the Leukemia and Lymphoma Society. M.W. is supported by a Human Frontiers Science Program Organization Fellowship. M.V. is supported by a grant from the Spanish Ministry of Science and Education. This work was supported in part by grants from the NIHGRI and NIGMS to R.A.Y. and from the NIH and NCI to R.J.

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Correspondence to Rudolf Jaenisch.

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T.I.L., D.K.G. and R.A.Y. consult for Agilent Technologies.

Supplementary information

Supplementary Notes

This file contains the Supplementary Methods and Supplementary Discussion; Supplementary Notes; Supplementary Figure Legends 1–9; Supplementary Figures 1–9. (PDF 9721 kb)

Supplementary Table 1

This file contains chromosomal coordinates for genomic regions bound by Suz12. (XLS 102 kb)

Supplementary Table 2

This file contains chromosomal coordinates for genomic regions bound by Eed. (XLS 69 kb)

Supplementary Table 3

This file contains chromosomal coordinates for genomic regions bound by Rnf2. (XLS 91 kb)

Supplementary Table 4

This file contains chromosomal coordinates for genomic regions bound by Phc1. (XLS 69 kb)

Supplementary Table 5

This file contains the assignment of bound genomic regions to annotated transcripts. (XLS 4189 kb)

Supplementary Table 6

This file contains data from the independent site specific validation used to estimate error rates in location analysis data. (XLS 53 kb)

Supplementary Table 7.

This file contains chromosomal coordinates for genomic regions bound by H3K27me3. (XLS 175 kb)

Supplementary Table 8

This file contains all enriched gene ontology classifications for bound genes. (XLS 103 kb)

Supplementary Table 9

This file contains the complete list of transcription factor genes bound by PcG proteins. (DOC 36 kb)

Supplementary Table 10

This file contains all oligo sequences and RT-PCR results in wild-type and eed mutant ES cells used to generate Figure 2 in the main text. (XLS 39 kb)

Supplementary Table 11

This file contains the microarray expression data used to analyse the expression of PcG bound genes in ES cells and during ES cell differentiation as displayed in Figure 3 in the main text. (XLS 6725 kb)

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

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