- Lewis, E. B. A gene complex controlling segmentation in Drosophila. Nature 276, 565–570 (1978).
Article CAS Google Scholar
- 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
- Morey, L. & Helin, K. Polycomb group protein-mediated repression of transcription. Trends Biochem. Sci. 35, 323–332 (2010).
Article CAS Google Scholar
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Kaustov, L. et al. Recognition and specificity determinants of the human cbx chromodomains. J. Biol. Chem. 286, 521–529 (2011).
Article CAS Google Scholar
- 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
- Kamminga, L. M. et al. The Polycomb group gene Ezh2 prevents hematopoietic stem cell exhaustion. Blood 107, 2170–2179 (2006).
Article CAS Google Scholar
- 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
- 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
- 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
- Dephoure, N. et al. A quantitative atlas of mitotic phosphorylation. Proc. Natl Acad. Sci. USA 105, 10762–10767 (2008).
Article CAS Google Scholar
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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).
- 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
- 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
- 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
- Gerrits, A. et al. Cellular barcoding tool for clonal analysis in the hematopoietic system. Blood 115, 2610–2618 (2010).
Article CAS Google Scholar
- 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
- 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
- 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
- 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
- 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
- Dietrich, N. et al. REST-mediated recruitment of polycomb repressor complexes in mammalian cells. PLoS Genet. 8, e1002494 (2012).
Article CAS Google Scholar
- 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
- Giardine, B. et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451–1455 (2005).
Article CAS Google Scholar
- Blankenberg, D. et al. Manipulation of FASTQ data with Galaxy. Bioinformatics 26, 1783–1785 (2010).
Article CAS Google Scholar
- 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
- Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
Article Google Scholar
- Feng, J., Liu, T. & Zhang, Y. Using MACS to identify peaks from ChIP-Seq data. Curr. Protoc. Bioinform. (2011) Chapter 2, Unit 2 14.
- 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
- 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
- de St Groth, Fazekas The evaluation of limiting dilution assays. J. Immunol. Methods 49, R11–R23 (1982).
Article Google Scholar