Changes in the Distributions and Dynamics of Polycomb Repressive Complexes during Embryonic Stem Cell Differentiation

REFERENCES

• Agger, K., P. A. Cloos, J. Christensen, D. Pasini, S. Rose, J. Rappsilber, I. Issaeva, E. Canaani, A. E. Salcini, and K. Helin. 2007. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449:731–734.
   PubMed Web of Science ®Google Scholar
• Akasaka, T., M. Kanno, R. Balling, M. A. Mieza, M. Taniguchi, and H. Koseki. 1996. A role for mel-18, a Polycomb group-related vertebrate gene, during the anteroposterior specification of the axial skeleton. Development 122:1513–1522.
   PubMed Web of Science ®Google Scholar
• Alkema, M. J., J. Jacobs, J. W. Voncken, N. A. Jenkins, N. G. Copeland, D. P. Satijn, A. P. Otte, A. Berns, and M. van Lohuizen. 1997. MPc2, a new murine homolog of the Drosophila Polycomb protein is a member of the mouse Polycomb transcriptional repressor complex. J. Mol. Biol. 273:993–1003.
   PubMedGoogle Scholar
• Bain, G., D. Kitchens, M. Yao, J. E. Huettner, and D. I. Gottlieb. 1995. Embryonic stem cells express neuronal properties in vitro. Dev. Biol. 168:342–357.
   PubMed Web of Science ®Google Scholar
• Bárdos, J. I., A. J. Saurin, C. Tissot, E. Duprez, and P. S. Freemont. 2000. HPC3 is a new human Polycomb orthologue that interacts and associates with RING1 and Bmi1 and has transcriptional repression properties. J. Biol. Chem. 275:28785–28792.
   PubMedGoogle Scholar
• Bernstein, E., E. M. Duncan, O. Masui, J. Gil, E. Heard, and C. D. Allis. 2006. Mouse Polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol. Cell. Biol. 26:2560–2569.
   PubMed Web of Science ®Google Scholar
• Boyer, L. A., D. Mathur, and R. Jaenisch. 2006. Molecular control of pluripotency. Curr. Opin. Genet. Dev. 16:455–462.
   PubMed Web of Science ®Google Scholar
• Boyer, L. A., K. Plath, J. Zeitlinger, T. Brambrink, L. A. Medeiros, T. I. Lee, S. S. Levine, M. Wernig, A. Tajonar, M. K. Ray, G. W. Bell, A. P. Otte, M. Vidal, D. K. Gifford, R. A. Young, and R. Jaenisch. 2006. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441:349–353.
   PubMed Web of Science ®Google Scholar
• Bracken, A. P., N. Dietrich, D. Pasini, K. H. Hansen, and K. Helin. 2006. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 20:1123–1136.
   PubMed Web of Science ®Google Scholar
• Buchenau, P., J. Hodgson, H. Strutt, and D. J. Arndt-Jovin. 1998. The distribution of Polycomb-group proteins during cell division and development in Drosophila embryos: impact on models for silencing. J. Cell Biol. 141:469–481.
   PubMed Web of Science ®Google Scholar
• Buszczak, M., and A. C. Spradling. 2006. Searching chromatin for stem cell identity. Cell 125:233–236.
   PubMedGoogle Scholar
• Cao, R., L. Wang, H. Wang, L. Xia, H. Erdjument-Bromage, P. Tempst, R. S. Jones, and Y. Zhang. 2002. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298:1039–1043.
   PubMed Web of Science ®Google Scholar
• Cheutin, T., A. J. McNairn, T. Jenuwein, D. M. Gilbert, P. B. Singh, and T. Misteli. 2003. Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299:721–725.
   PubMed Web of Science ®Google Scholar
• Coré, N., S. Bel, S. J. Gaunt, M. Aurrand-Lions, J. Pearce, A. Fisher, and M. Djabali. 1997. Altered cellular proliferation and mesoderm patterning in Polycomb-M33-deficient mice. Development 124:721–729.
   PubMed Web of Science ®Google Scholar
• Cui, B., Y. Liu, and M. A. Gorovsky. 2006. Deposition and function of histone H3 variants in Tetrahymena thermophila. Mol. Cell. Biol. 26:7719–7730.
   PubMedGoogle Scholar
• Dani, C., A. G. Smith, S. Dessolin, P. Leroy, L. Staccini, P. Villageois, C. Darimont, and G. Ailhaud. 1997. Differentiation of embryonic stem cells into adipocytes in vitro. J. Cell Sci. 110:1279–1285.
   PubMed Web of Science ®Google Scholar
• del Mar Lorente, M., C. Marcos-Gutierrez, C. Perez, J. Schoorlemmer, A. Ramirez, T. Magin, and M. Vidal. 2000. Loss- and gain-of-function mutations show a Polycomb group function for Ring1A in mice. Development 127:5093–5100.
   PubMedGoogle Scholar
• Dietrich, N., A. P. Bracken, E. Trinh, C. K. Schjerling, H. Koseki, J. Rappsilber, K. Helin, and K. H. Hansen. 2007. Bypass of senescence by the Polycomb group protein CBX8 through direct binding to the INK4A-ARF locus. EMBO J. 26:1637-1648
   PubMed Web of Science ®Google Scholar
• Festenstein, R., S. N. Pagakis, K. Hiragami, D. Lyon, A. Verreault, B. Sekkali, and D. Kioussis. 2003. Modulation of heterochromatin protein 1 dynamics in primary mammalian cells. Science 299:719–721.
   PubMed Web of Science ®Google Scholar
• Ficz, G., R. Heintzmann, and D. J. Arndt-Jovin. 2005. Polycomb group protein complexes exchange rapidly in living Drosophila. Development 132:3963–3976.
   PubMed Web of Science ®Google Scholar
• Gil, J., D. Bernard, D. Martinez, and D. Beach. 2004. Polycomb CBX7 has a unifying role in cellular lifespan. Nat. Cell Biol. 6:67–72.
   PubMed Web of Science ®Google Scholar
• Grimaud, C., F. Bantignies, M. Pal-Bhadra, P. Ghana, U. Bhadra, and G. Cavalli. 2006. RNAi components are required for nuclear clustering of Polycomb group response elements. Cell 124:957–971.
   PubMed Web of Science ®Google Scholar
• Hernández-Muñoz, I., P. Taghavi, C. Kuijl, J. Neefjes, and M. van Lohuizen. 2005. Association of BMI1 with Polycomb bodies is dynamic and requires PRC2/EZH2 and the maintenance DNA methyltransferase DNMT1. Mol. Cell. Biol. 25:11047–11058.
   PubMed Web of Science ®Google Scholar
• Hu, C. D., Y. Chinenov, and T. K. Kerppola. 2002. Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol. Cell 9:789–798.
   PubMed Web of Science ®Google Scholar
• Isono, K., Y. Fujimura, J. Shinga, M. Yamaki, J. O-Wang, Y. Takihara, Y. Murahashi, Y. Takada, Y. Mizutani-Koseki, and H. Koseki. 2005. Mammalian polyhomeotic homologues Phc2 and Phc1 act in synergy to mediate Polycomb repression of Hox genes. Mol. Cell. Biol. 25:6694–6706.
   PubMedGoogle Scholar
• Kagey, M. H., T. A. Melhuish, and D. Wotton. 2003. The Polycomb protein Pc2 is a SUMO E3. Cell 113:127–137.
   PubMed Web of Science ®Google Scholar
• Kerppola, T. K. 2006. Visualization of molecular interactions by fluorescence complementation. Nat. Rev. Mol. Cell Biol. 7:449–456.
   PubMed Web of Science ®Google Scholar
• Kuzmichev, A., K. Nishioka, H. Erdjument-Bromage, P. Tempst, and D. Reinberg. 2002. Histone methyltransferase activity associated with a human multiprotein complex containing the enhancer of Zeste protein. Genes Dev. 16:2893–2905.
   PubMed Web of Science ®Google Scholar
• Laricchia-Robbio, L., T. Tamura, T. Karpova, B. L. Sprague, J. G. McNally, and K. Ozato. 2005. Partner-regulated interaction of IFN regulatory factor 8 with chromatin visualized in live macrophages. Proc. Natl. Acad. Sci. USA 102:14368–14373.
   PubMedGoogle Scholar
• Lee, M. G., R. Villa, P. Trojer, J. Norman, K. P. Yan, D. Reinberg, L. Di Croce, and R. Shiekhattar. 2007. Demethylation of H3K27 regulates Polycomb recruitment and H2A ubiquitination. Science 318:447–450.
   PubMed Web of Science ®Google Scholar
• Lee, T. I., R. G. Jenner, L. A. Boyer, M. G. Guenther, S. S. Levine, R. M. Kumar, B. Chevalier, S. E. Johnstone, M. F. Cole, K. Isono, H. Koseki, T. Fuchikami, K. Abe, H. L. Murray, J. P. Zucker, B. Yuan, G. W. Bell, E. Herbolsheimer, N. M. Hannett, K. Sun, D. T. Odom, A. P. Otte, T. L. Volkert, D. P. Bartel, D. A. Melton, D. K. Gifford, R. Jaenisch, and R. A. Young. 2006. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125:301–313.
   PubMed Web of Science ®Google Scholar
• Lorente, M., C. Perez, C. Sanchez, M. Donohoe, Y. Shi, and M. Vidal. 2006. Homeotic transformations of the axial skeleton of YY1 mutant mice and genetic interaction with the Polycomb group gene Ring1/Ring1A. Mech. Dev. 123:312–320.
   PubMedGoogle Scholar
• Martinez, A. M., S. Colomb, J. Dejardin, F. Bantignies, and G. Cavalli. 2006. Polycomb group-dependent cyclin A repression in Drosophila. Genes Dev. 20:501–513.
   PubMedGoogle Scholar
• McNally, J. G., W. G. Muller, D. Walker, R. Wolford, and G. L. Hager. 2000. The glucocorticoid receptor: rapid exchange with regulatory sites in living cells. Science 287:1262–1265.
   PubMed Web of Science ®Google Scholar
• Meshorer, E., D. Yellajoshula, E. George, P. J. Scambler, D. T. Brown, and T. Misteli. 2006. Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev. Cell 10:105–116.
   PubMed Web of Science ®Google Scholar
• Nagai, T., K. Ibata, E. S. Park, M. Kubota, K. Mikoshiba, and A. Miyawaki. 2002. A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat. Biotechnol. 20:87–90.
   PubMed Web of Science ®Google Scholar
• Niwa, H., K. Yamamura, and J. Miyazaki. 1991. Efficient selection for high-expression transfectants with a novel eukaryotic vector. Gene 108:193–199.
   PubMed Web of Science ®Google Scholar
• O'Carroll, D., S. Erhardt, M. Pagani, S. C. Barton, M. A. Surani, and T. Jenuwein. 2001. The Polycomb-group gene Ezh2 is required for early mouse development. Mol. Cell. Biol. 21:4330–4336.
   PubMed Web of Science ®Google Scholar
• Pasini, D., A. P. Bracken, J. B. Hansen, M. Capillo, and K. Helin. 2007. The Polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol. Cell. Biol. 27:3769–3779.
   PubMed Web of Science ®Google Scholar
• Pearce, J. J., P. B. Singh, and S. J. Gaunt. 1992. The mouse has a Polycomb-like chromobox gene. Development 114:921–929.
   PubMedGoogle Scholar
• Penny, G. D., G. F. Kay, S. A. Sheardown, S. Rastan, and N. Brockdorff. 1996. Requirement for Xist in X chromosome inactivation. Nature 379:131–137.
   PubMed Web of Science ®Google Scholar
• Reid, G., M. R. Hubner, R. Metivier, H. Brand, S. Denger, D. Manu, J. Beaudouin, J. Ellenberg, and F. Gannon. 2003. Cyclic, proteasome-mediated turnover of unliganded and liganded ERalpha on responsive promoters is an integral feature of estrogen signaling. Mol. Cell 11:695–707.
   PubMed Web of Science ®Google Scholar
• Satijn, D. P., and A. P. Otte. 1999. RING1 interacts with multiple Polycomb-group proteins and displays tumorigenic activity. Mol. Cell. Biol. 19:57–68.
   PubMed Web of Science ®Google Scholar
• Saurin, A. J., C. Shiels, J. Williamson, D. P. Satijn, A. P. Otte, D. Sheer, and P. S. Freemont. 1998. The human Polycomb group complex associates with pericentromeric heterochromatin to form a novel nuclear domain. J. Cell Biol. 142:887–898.
   PubMed Web of Science ®Google Scholar
• Schmidt, U., K. Richter, A. B. Berger, and P. Lichter. 2006. In vivo BiFC analysis of Y14 and NXF1 mRNA export complexes: preferential localization within and around SC35 domains. J. Cell Biol. 172:373–381.
   PubMedGoogle Scholar
• Schoeftner, S., A. K. Sengupta, S. Kubicek, K. Mechtler, L. Spahn, H. Koseki, T. Jenuwein, and A. Wutz. 2006. Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing. EMBO J. 25:3110–3122.
   PubMed Web of Science ®Google Scholar
• Schoorlemmer, J., C. Marcos-Gutierrez, F. Were, R. Martinez, E. Garcia, D. P. Satijn, A. P. Otte, and M. Vidal. 1997. Ring1A is a transcriptional repressor that interacts with the Polycomb-M33 protein and is expressed at rhombomere boundaries in the mouse hindbrain. EMBO J. 16:5930–5942.
   PubMed Web of Science ®Google Scholar
• Schuettengruber, B., D. Chourrout, M. Vervoort, B. Leblanc, and G. Cavalli. 2007. Genome regulation by Polycomb and Trithorax proteins. Cell 128:735–745.
   PubMed Web of Science ®Google Scholar
• Schumacher, A., C. Faust, and T. Magnuson. 1996. Positional cloning of a global regulator of anterior-posterior patterning in mice. Nature 383:250.
   PubMedGoogle Scholar
• Schwartz, Y. B., and V. Pirrotta. 2007. Polycomb silencing mechanisms and the management of genomic programmes. Nat. Rev. Genet. 8:9–22.
   PubMed Web of Science ®Google Scholar
• Scott, C. L., J. Gil, E. Hernando, J. Teruya-Feldstein, M. Narita, D. Martinez, T. Visakorpi, D. Mu, C. Cordon-Cardo, G. Peters, D. Beach, and S. W. Lowe. 2007. Role of the chromobox protein CBX7 in lymphomagenesis. Proc. Natl. Acad. Sci. USA 104:5389–5394.
   PubMed Web of Science ®Google Scholar
• Shao, Z., F. Raible, R. Mollaaghababa, J. R. Guyon, C. T. Wu, W. Bender, and R. E. Kingston. 1999. Stabilization of chromatin structure by PRC1, a Polycomb complex. Cell 98:37–46.
   PubMedGoogle Scholar
• Smith, A. G. 1991. Culture and differentiation of embryonic stem cells. J. Tissue Cult. Methods 13:89–94.
   Google Scholar
• Suzuki, M., Y. Mizutani-Koseki, Y. Fujimura, H. Miyagishima, T. Kaneko, Y. Takada, T. Akasaka, H. Tanzawa, Y. Takihara, M. Nakano, H. Masumoto, M. Vidal, K. Isono, and H. Koseki. 2002. Involvement of the Polycomb-group gene Ring1B in the specification of the anterior-posterior axis in mice. Development 129:4171–4183.
   PubMedGoogle Scholar
• Takihara, Y., D. Tomotsune, M. Shirai, Y. Katoh-Fukui, K. Nishii, M. A. Motaleb, M. Nomura, R. Tsuchiya, Y. Fujita, Y. Shibata, T. Higashinakagawa, and K. Shimada. 1997. Targeted disruption of the mouse homologue of the Drosophila polyhomeotic gene leads to altered anteroposterior patterning and neural crest defects. Development 124:3673–3682.
   PubMedGoogle Scholar
• van der Lugt, N. M., J. Domen, K. Linders, M. van Roon, E. Robanus-Maandag, H. te Riele, M. van der Valk, J. Deschamps, M. Sofroniew, M. van Lohuizen, et al. 1994. Posterior transformation, neurological abnormalities, and severe hematopoietic defects in mice with a targeted deletion of the bmi-1 proto-oncogene. Genes Dev. 8:757–769.
   PubMed Web of Science ®Google Scholar
• Voncken, J. W., B. A. Roelen, M. Roefs, S. de Vries, E. Verhoeven, S. Marino, J. Deschamps, and M. van Lohuizen. 2003. Rnf2 (Ring1b) deficiency causes gastrulation arrest and cell cycle inhibition. Proc. Natl. Acad. Sci. USA 100:2468–2473.
   PubMed Web of Science ®Google Scholar
• Voncken, J. W., D. Schweizer, L. Aagaard, L. Sattler, M. F. Jantsch, and M. van Lohuizen. 1999. Chromatin-association of the Polycomb group protein BMI1 is cell cycle-regulated and correlates with its phosphorylation status. J. Cell Sci. 112:4627–4639.
   PubMed Web of Science ®Google Scholar
• Wang, L., J. L. Brown, R. Cao, Y. Zhang, J. A. Kassis, and R. S. Jones. 2004. Hierarchical recruitment of Polycomb group silencing complexes. Mol. Cell 14:637–646.
   PubMed Web of Science ®Google Scholar
• Yao, J., K. M. Munson, W. W. Webb, and J. T. Lis. 2006. Dynamics of heat shock factor association with native gene loci in living cells. Nature 442:1050–1053.
   PubMedGoogle Scholar