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Polycomb Cbx family members mediate the balance between haematopoietic stem cell self-renewal and differentiation

Abstract

The balance between self-renewal and differentiation of adult stem cells is essential for tissue homeostasis. Here we show that in the haematopoietic system this process is governed by polycomb chromobox (Cbx) proteins. Cbx7 is specifically expressed in haematopoietic stem cells (HSCs), and its overexpression enhances self-renewal and induces leukaemia. This effect is dependent on integration into polycomb repressive complex-1 (PRC1) and requires H3K27me3 binding. In contrast, overexpression of Cbx2, Cbx4 or Cbx8 results in differentiation and exhaustion of HSCs. ChIP-sequencing analysis shows that Cbx7 and Cbx8 share most of their targets; we identified approximately 200 differential targets. Whereas genes targeted by Cbx8 are highly expressed in HSCs and become repressed in progenitors, Cbx7 targets show the opposite expression pattern. Thus, Cbx7 preserves HSC self-renewal by repressing progenitor-specific genes. Taken together, the presence of distinct Cbx proteins confers target selectivity to PRC1 and provides a molecular balance between self-renewal and differentiation of HSCs.

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Figure 1: Enforced expression of Cbx genes reveals distinct effects on in vitro progenitor and HSC potential.
Figure 2: Cbx7 induces distinct types of leukaemia, whereas Cbx2, Cbx4 and Cbx8 induce a competitive disadvantage in vivo.
Figure 3: Cbx7 increases the proliferative capacity of purified multipotent haematopoietic subsets.
Figure 4: Cbx7 induces self-renewal of LT-HSCs, ST-HSCs and MPPs, but not of lineage restricted progenitors.
Figure 5: Cbx7 is required for HSPC self-renewal.
Figure 6: Cbx7-induced self-renewal requires PRC1 integration and H3K27me3 binding.
Figure 7: Cbx7 and Cbx8 targets are coordinately regulated during HSC differentiation and show reciprocal expression patterns.

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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. Mechanisms of polycomb gene silencing: knowns and unknowns. Nat. Rev. Mol. Cell Biol. 10, 697–708 (2009).

    Article  CAS  Google Scholar 

  3. Morey, L. & Helin, K. Polycomb group protein-mediated repression of transcription. Trends Biochem. Sci. 35, 323–332 (2010).

    Article  CAS  Google Scholar 

  4. Lessard, J., Baban, S. & Sauvageau, G. Stage-specific expression of polycomb group genes in human BM cells. Blood 91, 1216–1224 (1998).

    CAS  PubMed  Google Scholar 

  5. Gunster, M. J. et al. Differential expression of human Polycomb groupproteins in various tissues and cell types. J. Cell. Biochem. Suppl. 36, 129–143 (2001).

    Article  Google Scholar 

  6. Iwama, A. et al. Enhanced self-renewal of hematopoietic stem cells mediated by the polycomb gene product Bmi-1. Immunity 21, 843–851 (2004).

    Article  CAS  Google Scholar 

  7. Kato, Y., Koseki, H., Vidal, M., Nakauchi, H. & Iwama, A. Unique composition of polycomb repressive complex 1 in hematopoietic stem cells. Int. J. Hematol. 85, 179–181 (2007).

    Article  CAS  Google Scholar 

  8. Morey, L. et al. Nonoverlapping functions of the Polycomb group Cbx family of proteins in embryonic stem cells. Cell Stem Cell 10, 47–62 (2012).

    Article  CAS  Google Scholar 

  9. Tavares, L. et al. RYBP-PRC1 complexes mediate H2A ubiquitylation atpolycomb target sites independently of PRC2 and H3K27me3. Cell 148, 664–678 (2012).

    Article  CAS  Google Scholar 

  10. O’Loghlen, A. et al. MicroRNA regulation of Cbx7 mediates a switch of Polycomb orthologs during ESC differentiation. Cell Stem Cell 10, 33–46 (2012).

    Article  Google Scholar 

  11. Gao, Z. et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol. Cell 45, 344–356 (2012).

    Article  CAS  Google Scholar 

  12. Maertens, G. N. et al. Several distinct polycomb complexes regulate and co-localize on the INK4a tumor suppressor locus. PLoS One 4, e6380 (2009).

    Article  Google Scholar 

  13. Vandamme, J., Volkel, P., Rosnoblet, C., Le Faou, P. & Angrand, P. O. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. Mol. Cell Proteomics 10, M110.002642 (2011).

    Article  Google Scholar 

  14. Min, J., Zhang, Y. & Xu, R. M. Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev. 17, 1823–1828 (2003).

    Article  CAS  Google Scholar 

  15. Fischle, W. et al. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 17, 1870–1881 (2003).

    Article  CAS  Google Scholar 

  16. Bernstein, E. et al. Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol. Cell Biol. 26, 2560–2569 (2006).

    Article  CAS  Google Scholar 

  17. Kaustov, L. et al. Recognition and specificity determinants of the human cbx chromodomains. J. Biol. Chem. 286, 521–529 (2011).

    Article  CAS  Google Scholar 

  18. Van Lohuizen, M. et al. Identification of cooperating oncogenes in E mu-myc transgenic mice by provirus tagging. Cell 65, 737–752 (1991).

    Article  CAS  Google Scholar 

  19. Kamminga, L. M. et al. The Polycomb group gene Ezh2 prevents hematopoietic stem cell exhaustion. Blood 107, 2170–2179 (2006).

    Article  CAS  Google Scholar 

  20. Lessard, J. et al. Functional antagonism of the Polycomb-Group genes eed and Bmi1 in hemopoietic cell proliferation. Genes Dev. 13, 2691–2703 (1999).

    Article  CAS  Google Scholar 

  21. Park, I. K. et al. Bmi-1 is required for maintenance of adult self-renewing haematopoietic stem cells. Nature 423, 302–305 (2003).

    Article  CAS  Google Scholar 

  22. Rizo, A., Dontje, B., Vellenga, E., de Haan, G. & Schuringa, J. J. Long-term maintenance of human hematopoietic stem/progenitor cells by expression of BMI1. Blood 111, 2621–2630 (2008).

    Article  CAS  Google Scholar 

  23. Dephoure, N. et al. A quantitative atlas of mitotic phosphorylation. Proc. Natl Acad. Sci. USA 105, 10762–10767 (2008).

    Article  CAS  Google Scholar 

  24. Scott, C. L. et al. Role of the chromobox protein CBX7 in lymphomagenesis. Proc. Natl Acad. Sci. USA 104, 5389–5394 (2007).

    Article  CAS  Google Scholar 

  25. Ploemacher, R. E., van der Sluijs, J. P., van Beurden, C. A., Baert, M. R. & Chan, P. L. Use of limiting-dilution type long-term marrow cultures in frequency analysis of marrow-repopulating and spleen colony-forming hematopoietic stem cells in the mouse. Blood 78, 2527–2533 (1991).

    CAS  PubMed  Google Scholar 

  26. De Haan, G., Nijhof, W. & Van Zant, G. Mouse strain-dependent changes in frequency and proliferation of hematopoietic stem cells during aging: correlation between lifespan and cycling activity. Blood 89, 1543–1550 (1997).

    CAS  PubMed  Google Scholar 

  27. Gil, J., Bernard, D., Martinez, D. & Beach, D. Polycomb CBX7 has a unifying role in cellular lifespan. Nat. Cell Biol. 6, 67–72 (2004).

    Article  CAS  Google Scholar 

  28. Jacobs, J. J., Kieboom, K., Marino, S., DePinho, R. A. & van Lohuizen, M. The oncogene and Polycomb-group gene bmi-1 regulates cell proliferation and senescence through the ink4a locus. Nature 397, 164–168 (1999).

    Article  CAS  Google Scholar 

  29. Oguro, H. et al. Differential impact of Ink4a and Arf on hematopoietic stem cells and their BM microenvironment in Bmi1-deficient mice. J. Exp. Med. 203, 2247–2253 (2006).

    Article  CAS  Google Scholar 

  30. Voy, B. H. et al. Extracting gene networks for low-dose radiation using graph theoretical algorithms. PLoS Comput. Biol. 2, e89 (2006).

    Article  Google Scholar 

  31. Walasek, M. A. et al. The combination of valproic acid and lithiumdelays hematopoietic stem/progenitor cell differentiation. Blood 119, 3050–3059 (2012).

    Article  CAS  Google Scholar 

  32. Colombo, E., Alcalay, M. & Pelicci, P. G. Nucleophosmin and its complex network: a possible therapeutic target in hematological diseases. Oncogene 30, 2595–2609 (2011).

    Article  CAS  Google Scholar 

  33. Falini, B. et al. Acute myeloid leukemia with mutated nucleophosmin (NPM1): any hope for a targeted therapy? Blood Rev. 25, 247–254 (2011).

    Article  CAS  Google Scholar 

  34. Yin, B. et al. A retroviral mutagenesis screen reveals strong cooperation between Bcl11a overexpression and loss of the Nf1 tumor suppressor gene. Blood 113, 1075–1085 (2009).

    Article  CAS  Google Scholar 

  35. Deambrogi, C. et al. Analysis of the REL, BCL11A, and MYCN proto-oncogenes belonging to the 2p amplicon in chronic lymphocytic leukemia. Am. J. Hematol. 85, 541–544 (2010).

    Article  CAS  Google Scholar 

  36. Osawa, M. et al. Erythroid expansion mediated by the Gfi-1B zinc finger protein: role in normal hematopoiesis. Blood 100, 2769–2777 (2002).

    Article  CAS  Google Scholar 

  37. Laurent, B. et al. High-mobility group protein HMGB2 regulates human erythroid differentiation through trans-activation of GFI1B transcription. Blood 115, 687–695 (2010).

    Article  CAS  Google Scholar 

  38. Van der Meer, L. T., Jansen, J. H. & van der Reijden, B. A. Gfi1 and Gfi1b: key regulators of hematopoiesis. Leukemia 24, 1834–1843 (2010).

    Article  CAS  Google Scholar 

  39. Luis, N. M. et al. Regulation of human epidermal stem cell proliferation and senescence requires polycomb- dependent and -independent functions of Cbx4. Cell Stem Cell 9, 233–246 (2011).

    Article  CAS  Google Scholar 

  40. Bastian, M., Heymann, S. & Jacomy, M. Gephi: an open source software for exploring and manipulating networks. Int. AAAI Conf. on Weblogs and Social Media (2009).

  41. Dykstra, B., Olthof, S., Schreuder, J., Ritsema, M. & de Haan, G. Clonal analysis reveals multiple functional defects of aged murine hematopoietic stem cells. J. Exp. Med. 208, 2691–2703 (2011).

    Article  CAS  Google Scholar 

  42. Challen, G. A., Boles, N., Lin, K. K. & Goodell, M. A. Mouse hematopoietic stem cell identification and analysis. Cytometry A 75, 14–24 (2009).

    Article  Google Scholar 

  43. Dietrich, N. et al. Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A-ARF locus. EMBO J. 26, 1637–1648 (2007).

    Article  CAS  Google Scholar 

  44. Gerrits, A. et al. Cellular barcoding tool for clonal analysis in the hematopoietic system. Blood 115, 2610–2618 (2010).

    Article  CAS  Google Scholar 

  45. Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283–1298 (2006).

    Article  CAS  Google Scholar 

  46. Sarbassov, D. D., Guertin, D. A., Ali, S. M. & Sabatini, D. M. Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complex. Science 307, 1098–1101 (2005).

    Article  CAS  Google Scholar 

  47. Van Os, R. P., Dethmers-Ausema, B. & de Haan, G. In vitro assays forcobblestone area-forming cells, LTC-IC, and CFU-C. Methods Mol. Biol. 430, 143–157 (2008).

    Article  CAS  Google Scholar 

  48. Frank, S. R., Schroeder, M., Fernandez, P., Taubert, S. & Amati, B. Binding of c-Myc to chromatin mediates mitogen-induced acetylation of histone H4 and gene activation. Genes Dev. 15, 2069–2082 (2001).

    Article  CAS  Google Scholar 

  49. 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).

    Article  CAS  Google Scholar 

  50. Dietrich, N. et al. REST-mediated recruitment of polycomb repressor complexes in mammalian cells. PLoS Genet. 8, e1002494 (2012).

    Article  CAS  Google Scholar 

  51. Bracken, A. P. et al. The Polycomb group proteins bind throughout the INK4a-ARF locus and are disassociated in senescent cells. Genes Dev. 21, 525–530 (2007).

    Article  CAS  Google Scholar 

  52. Giardine, B. et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451–1455 (2005).

    Article  CAS  Google Scholar 

  53. Blankenberg, D. et al. Manipulation of FASTQ data with Galaxy. Bioinformatics 26, 1783–1785 (2010).

    Article  CAS  Google Scholar 

  54. Goecks, J., Nekrutenko, A. & Taylor, J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).

    Article  Google Scholar 

  55. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).

    Article  Google Scholar 

  56. Feng, J., Liu, T. & Zhang, Y. Using MACS to identify peaks from ChIP-Seq data. Curr. Protoc. Bioinform. (2011) Chapter 2, Unit 2 14.

  57. Zhu, L. J. et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinform. 11, 237 (2010).

    Article  Google Scholar 

  58. Durinck, S., Spellman, P. T., Birney, E. & Huber, W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protoc. 4, 1184–1191 (2009).

    Article  CAS  Google Scholar 

  59. de St Groth, Fazekas The evaluation of limiting dilution assays. J. Immunol. Methods 49, R11–R23 (1982).

    Article  Google Scholar 

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Acknowledgements

We thank H. Moes, G. Mesander, H. de Bruin and R. J. van der Lei for expert flow cytometry assistance, the entire staff of the Central Animal Facility at the UMCG, K. Magnussen from the National High-throughput Sequencing Centre of the University of Copenhagen, B. Dethmers-Ausema, R. Bron, F. Feringa, K. van der Laan, V. Stojanovska and K. Wakker for laboratory assistance, J. Engelbert for bioinformatical assistance, and B. Dykstra, M. Niemantsverdriet, R. van Os and H. Schepers for valuable scientific discussions. We also acknowledge financial support from the Netherlands Organization for Scientific Research (VICI 918-76-601 and ALW to G.d.H), the Netherlands Institute for Regenerative Medicine, the Dutch Cancer Society (grant 2007-3729, and UMCG-2011-5277 to S.B.) and the European Community (EuroSystem, 200720). The work in the Helin laboratory was supported by the Danish National Research Foundation, the Novo Nordisk Foundation and the Danish Cancer Society.

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K.K., L.B., K.H. and G.d.H. initiated research and developed the concept of the paper. K.K., L.B., and G.d.H. designed research; K.K. and V.R. performed experiments with contributions from M.B., E.W., S.O., M.R., S.B. and X.W; E.Z. performed bioinformatics analyses with contributions from L.B. and K.K.; K.K. and L.B. analysed and interpreted data; and K.K. wrote the manuscript with contributions from L.B., K.H. and G.d.H.

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Correspondence to Gerald de Haan.

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Klauke, K., Radulović, V., Broekhuis, M. et al. Polycomb Cbx family members mediate the balance between haematopoietic stem cell self-renewal and differentiation. Nat Cell Biol 15, 353–362 (2013). https://doi.org/10.1038/ncb2701

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