Systems biology of stem cell fate and cellular reprogramming (original) (raw)

• Gage, F. Mammalian neural stem cells. Science 287, 1433–1438 (2000).
  Article CAS PubMed Google Scholar
• Wagers, A. & Weissman, I. Plasticity of adult stem cells. Cell 116, 639–648 (2004).
  Article CAS PubMed Google Scholar
• Pittenger, M. et al. Multilineage potential of adult human mesenchymal stem cells. Science 284, 143–161 (1999).
  Article CAS PubMed Google Scholar
• Weissman, I. L. Translating stem and progenitor cell biology to the clinic: barriers and opportunities. Science 287, 1442–1446 (2000).
  Article CAS PubMed Google Scholar
• Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).
  Article CAS PubMed Google Scholar
• Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861–872 (2007).
  Article CAS PubMed Google Scholar
• Xie, H., Ye, M., Feng, R. & Graf, T. Stepwise reprogramming of B cells into macrophages. Cell 117, 663–676 (2004).
  Article CAS PubMed Google Scholar
• Zhou, Q., Brown, J., Kanarek, A., Rajagopal, J. & Melton, D. A. In vivo reprogramming of adult pancreatic exocrine cells to β-cells. Nature 455, 627–632 (2008).
  Article CAS PubMed Google Scholar
• Hanna, J. et al. Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skin. Science 318, 1920–1923 (2007).
  Article CAS PubMed Google Scholar
• Loh, Y. et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nature Genet. 38, 431–440 (2006).
  Article CAS PubMed Google Scholar
• Boyer, L. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Kim, J., Chu, J., Shen, X., Wang, J. & Orkin, S. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049–1061 (2008).
  Article CAS PubMed Google Scholar
• Avilion, A. A. et al. Multipotent cell lineages in early mouse development depend on SOX2 function. Genes Dev. 17, 126–140 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Chambers, I. et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 113, 643–655 (2003).
  Article CAS PubMed Google Scholar
• Nichols, J. et al. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95, 379–391 (1998).
  Article CAS PubMed Google Scholar
• Mitsui, K. et al. The homeoprotein nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113, 631–642 (2003).
  Article CAS PubMed Google Scholar
• Wang, J. et al. A protein interaction network for pluripotency of embryonic stem cells. Nature 444, 364–368 (2006). This study derives a high-confidence protein–protein interaction network in ES cells centred around the transcription factor NANOG.
  CAS Google Scholar
• Muller, F.-J. et al. Regulatory networks define phenotypic classes of human stem cell lines. Nature 455, 401–405 (2008). This study uses innovative computational techniques to derive an extended network for stem cell pluripotency.
  Article PubMed PubMed Central CAS Google Scholar
• Aderem, A. Systems biology: its practice and challenges. Cell 121, 511–513 (2005).
  Article CAS PubMed Google Scholar
• Kitano, H. Computational systems biology. Nature 420, 206–210 (2002).
  Article CAS PubMed Google Scholar
• Kirschner, M. W. The meaning of systems biology. Cell 121, 503–504 (2005).
  Article CAS PubMed Google Scholar
• Kitano, H. Systems biology: a brief overview. Science 295, 1662–1664 (2002).
  Article CAS PubMed Google Scholar
• Alon, U. An introduction to systems biology: design principles of biological circuits (Chapman & Hall/CRC, Boca Raton, 2007).
  Google Scholar
• Sontag, E. Mathematical control theory (Springer, New York, 1998).
  Book Google Scholar
• Wiggins, S. Introduction to applied nonlinear dynamical systems and chaos (Springer, New York, 2003).
  Google Scholar
• McQuarrie, D. & Allan, D. Statistical mechanics (University Science Books, Sausalito, 2000).
  Google Scholar
• Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002).
  Article CAS PubMed Google Scholar
• Ihmels, J. et al. Revealing modular organization in the yeast transcriptional network. Nature Genet. 31, 370–378 (2002).
  Article CAS PubMed Google Scholar
• Shen-Orr, S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31, 64–68 (2002).
  Article CAS PubMed Google Scholar
• Isalan, M. et al. Evolvability and hierarchy in rewired bacterial gene networks. Nature 452, 840–845 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Kidder, B. L., Yang, J. & Palmer, S. Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells. PLoS ONE 3, e3932 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106–1117 (2008).
  Article CAS PubMed Google Scholar
• Spooncer, E. et al. Developmental fate determination and marker discovery in hematopoietic stem cell biology using proteomic fingerprinting. Mol. Cell. Proteomics 7, 573–581 (2008).
  Article CAS PubMed Google Scholar
• Hinsby, A. M., Olsen, J. V. & Mann, M. Tyrosine phosphoproteomics of fibroblast growth factor signaling: a role for insulin receptor substrate-4. J. Biol. Chem. 279, 46438–46447 (2004).
  Article CAS PubMed Google Scholar
• Harary, F. Graph theory (Westview, Boulder, 1994).
  Google Scholar
• Tyson, J. J., Chen, K. & Novak, B. Network dynamics and cell physiology. Nature Rev. Mol. Cell Biol. 2, 908–916 (2001).
  Article CAS Google Scholar
• Ma'ayan, A. et al. Formation of regulatory patterns during signal propagation in a mammalian cellular network. Science 309, 1078–1083 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Bromberg, K. D., Ma'ayan, A., Neves, S. R. & Iyengar, R. Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science 320, 903–909 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Rual, J.-F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173–1178 (2005).
  Article CAS PubMed Google Scholar
• Barrios-Rodiles, M. et al. High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307, 1621–1625 (2005).
  Article CAS PubMed Google Scholar
• Basso, K. et al. Reverse engineering of regulatory networks in human B cells. Nature Genet. 37, 382–390 (2005).
  Article CAS PubMed Google Scholar
• Ma'ayan, A. Network integration and graph analysis in mammalian molecular systems biology. IET Syst. Biol. 2, 206–221 (2008).
  Article CAS PubMed Google Scholar
• Bansal, M., Belcastro, V., Ambesi-Impiombato, A. & di Bernardo, D. How to infer gene networks from expression profiles. Mol. Syst. Biol. 3, 78 (2007).
  Article PubMed PubMed Central Google Scholar
• D'haeseleer, P., Liang, S. & Somogyi, R. Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16, 707–726 (2000).
  Article CAS PubMed Google Scholar
• Berger, S., Posner, J. & Ma'ayan, A. Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics 8, 372 (2007).
  Article PubMed PubMed Central CAS Google Scholar
• Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Jiang, J. et al. A core Klf circuitry regulates self-renewal of embryonic stem cells. Nature Cell Biol. 10, 353–360 (2008).
  Article PubMed CAS Google Scholar
• Singh, S. K., Kagalwala, M. N., Parker-Thornburg, J., Adams, H. & Majumder, S. REST maintains self-renewal and pluripotency of embryonic stem cells. Nature 453, 223–227 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Cole, M., Johnstone, S., Newman, J., Kagey, M. & Young, R. Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev. 22, 746–755 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Liu, X. et al. Yamanaka factors critically regulate the developmental signaling network in mouse embryonic stem cells. Cell Res. 18, 1177–1189 (2008).
  Article CAS PubMed Google Scholar
• Marson, A. et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521–533 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Mackay, J. P., Sunde, M., Lowry, J. A., Crossley, M. & Matthews, J. M. Protein interactions: is seeing believing? Trends Biochem. Sci. 32, 530–531 (2007).
  Article CAS PubMed Google Scholar
• Ji, H., Vokes, S. A. & Wong, W. H. A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors. Nucleic Acids Res. 34, e146 (2006).
  Article PubMed PubMed Central CAS Google Scholar
• Ulitsky, I. & Shamir, R. Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol. 1, 8 (2007).
  Article PubMed PubMed Central CAS Google Scholar
• Mathur, D. et al. Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET. Genome Biol. 9, R126 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Boyer, L. A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349–353 (2006).
  Article CAS PubMed Google Scholar
• Johnson, R. et al. REST regulates distinct transcriptional networks in embryonic and neural stem cells. PLoS Biol. 6, e256 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Hu, G. et al. A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev. 23, 837–848 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Venkatesan, K. et al. An empirical framework for binary interactome mapping. Nature Methods 6, 83–90 (2009).
  Article CAS PubMed Google Scholar
• Paddison, P. J. et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 428, 427–431 (2004).
  Article CAS PubMed Google Scholar
• Ding, L. et al. A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Cell Stem Cell 4, 403–415 (2009).
  Article CAS PubMed Google Scholar
• Mogilner, A., Wollman, R. & Marshall, W. F. Quantitative modeling in cell biology: what is it good for? Dev. Cell 11, 279–287 (2006).
  Article CAS PubMed Google Scholar
• Wilkinson, D. J. Stochastic modelling for quantitative description of heterogeneous biological systems. Nature Rev. Genet. 10, 122–133 (2009).
  Article CAS PubMed Google Scholar
• Hasty, J., McMillen, D., Isaacs, F. & Collins, J. J. Computational studies of gene regulatory networks: in numero molecular biology. Nature Rev. Genet. 2, 268–279 (2001).
  Article CAS PubMed Google Scholar
• Kauffman, S. A. The origins of order: self-organization and selection in evolution (Oxford Univ. Press, 1993).
  Google Scholar
• Huang, A., Hu, L., Kauffman, S., Zhang, W. & Shmulevich, I. Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. BMC Syst. Biol. 3, 20 (2009).
  Article PubMed PubMed Central CAS Google Scholar
• Bar-Yam, Y., Harmon, D. & de Bivort, B. Systems biology: attractors and democratic dynamics. Science 323, 1016–1017 (2009).
  Article CAS PubMed Google Scholar
• Chang, H., Oh, P., Ingber, D. & Huang, S. Multistable and multistep dynamics in neutrophil differentiation. BMC Cell Biol. 7, 11 (2006).
  Article PubMed PubMed Central CAS Google Scholar
• Huang, S. & Ingber, D. A non-genetic basis for cancer progression and metastasis: self-organizing attractors in cell regulatory networks. Breast Dis. 26, 27–54 (2007).
  Article Google Scholar
• Kramer, B. P. & Fussenegger, M. Hysteresis in a synthetic mammalian gene network. Proc. Natl Acad. Sci. USA 102, 9517–9522 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Brock, A., Chang, H. & Huang, S. Non-genetic heterogeneity — a mutation-independent driving force for the somatic evolution of tumours. Nature Rev. Genet. 10, 336–342 (2009).
  Article CAS PubMed Google Scholar
• Enver, T., Pera, M., Peterson, C. & Andrews, P. W. Stem cell states, fates, and the rules of attraction. Cell Stem Cell 4, 387–397 (2009).
  Article CAS PubMed Google Scholar
• Delbruck, M. in Unités biologiques douées de continuité génétique 33–35 (Editions du Centre National de la Recherche Scientifique, Paris, 1949).
  Google Scholar
• Thomas, R. Laws for the dynamics of regulatory networks. Int. J. Dev. Biol. 42, 479–485 (1998).
  CAS PubMed Google Scholar
• Waddington, C. Organisers & genes (Cambridge Univ. Press, Cambridge, UK, 1940).
  Google Scholar
• Waddington, C. The strategy of the genes. (George Allen & Unwin, London,1957).
  Google Scholar
• Waddington, C. H. in The Development of Animal Behavior: a Reader (eds Bolhuis, J. J. & Hogan, J. A.) 22 (Blackwell, Oxford, 1999).
  Google Scholar
• Milnor, J. On the concept of attractor. Commun. Math. Phys. 99, 177–195 (1985).
  Article Google Scholar
• Strogatz, S. H. Nonlinear dynamics and chaos: with applications to physics, biology, chemistry, and engineering (Westview, Boulder, 2000).
  Google Scholar
• Kauffman, S. Homeostasis and differentiation in random genetic control networks. Nature 224, 177–178 (1969).
  Article CAS PubMed Google Scholar
• MacArthur, B. D., Please, C. P. & Oreffo, R. O. C. Stochasticity and the molecular mechanisms of induced pluripotency. PLoS ONE 3, e3086 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Chickarmane, V., Troein, C., Nuber, U. A., Sauro, H. M. & Peterson, C. Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput. Biol. 2, e123 (2006).
  Article PubMed PubMed Central CAS Google Scholar
• Cinquin, O. & Demongeot, J. High-dimensional switches and the modelling of cellular differentiation. J. Theor. Biol. 233, 391–411 (2005).
  Article CAS PubMed Google Scholar
• Chang, H. H., Hemberg, M., Barahona, M., Ingber, D. E. & Huang, S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 453, 544–547 (2008). This paper provides evidence of coexisting mammalian attractor states and switching between coexisting attractors at the single cell level owing to transcriptome-wide fluctuations in protein expression levels.
  Article CAS PubMed PubMed Central Google Scholar
• Huang, S., Eichler, G., Bar-Yam, Y. & Ingber, D. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys. Rev. Lett. 94, 128701 (2005). This study provides the first experimental evidence that a mammalian cell type corresponds to a high-dimensional attractor of an underlying dynamical system.
  Article PubMed CAS Google Scholar
• Xiong, W. & Ferrell, J. E. A positive-feedback-based bistable “memory module” that governs a cell fate decision. Nature 426, 460–465 (2003).
  Article CAS PubMed Google Scholar
• Becskei, A., Séraphin, B. & Serrano, L. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J. 20, 2528–2535 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Ferrell, J. E. Jr & Machleder, E. M. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280, 895–898 (1998).
  Article CAS PubMed Google Scholar
• Graf, T. & Stadtfeld, M. Heterogeneity of embryonic and adult stem cells. Cell Stem Cell 3, 480–483 (2008).
  Article CAS PubMed Google Scholar
• Ying, Q.-L. et al. The ground state of embryonic stem cell self-renewal. Nature 453, 519–523 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Sigal, A. et al. Variability and memory of protein levels in human cells. Nature 444, 643–646 (2006).
  Article CAS PubMed Google Scholar
• Till, J. E., McCulloch, E. A. & Siminovitch, L. A stochastic model of stem cell proliferation, based on the growth of spleen colony-forming cells. Proc. Natl Acad. Sci. USA 51, 29–36 (1964).
  Article CAS PubMed PubMed Central Google Scholar
• Suda, T., Suda, J. & Ogawa, M. Disparate differentiation in mouse hemopoietic colonies derived from paired progenitors. Proc. Natl Acad. Sci. USA 81, 2520–2524 (1984).
  Article CAS PubMed PubMed Central Google Scholar
• Ogawa, M., Porter, P. & Nakahata, T. Renewal and commitment to differentiation of hemopoietic stem cells (an interpretive review). Blood 61, 823–829 (1983).
  Article CAS PubMed Google Scholar
• Suda, T., Suda, J. & Ogawa, M. Single-cell origin of mouse hemopoietic colonies expressing multiple lineages in variable combinations. Proc. Natl Acad. Sci. USA 80, 6689–6693 (1983).
  Article CAS PubMed PubMed Central Google Scholar
• McAdams, H. H. & Arkin, A. Stochastic mechanisms in gene expression. Proc. Natl Acad. Sci. USA 94, 814–819 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Swain, P. S., Elowitz, M. B. & Siggia, E. D. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl Acad. Sci. USA 99, 12795–12800 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Arias, A. M. & Hayward, P. Filtering transcriptional noise during development: concepts and mechanisms. Nature Rev. Genet. 7, 34–44 (2006).
  Article CAS PubMed Google Scholar
• Zwaka, T. P. Keeping the noise down in ES cells. Cell 127, 1301–1302 (2006).
  Article CAS PubMed Google Scholar
• Szutorisz, H., Georgiou, A., Tora, L. & Dillon, N. The proteasome restricts permissive transcription at tissue-specific gene loci in embryonic stem cells. Cell 127, 1375–1388 (2006).
  Article CAS PubMed Google Scholar
• Chi, A. S. & Bernstein, B. E. Developmental biology: pluripotent chromatin state. Science 323, 220–221 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Austin, D. W. et al. Gene network shaping of inherent noise spectra. Nature 439, 608–611 (2006).
  Article CAS PubMed Google Scholar
• Thattai, M. & van Oudenaarden, A. Intrinsic noise in gene regulatory networks. Proc. Natl Acad. Sci. USA 98, 8614–8619 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Kaern, M., Elston, T. C., Blake, W. J. & Collins, J. J. Stochasticity in gene expression: from theories to phenotypes. Nature Rev. Genet. 6, 451–464 (2005).
  Article CAS PubMed Google Scholar
• Thattai, M. & van Oudenaarden, A. Stochastic gene expression in fluctuating environments. Genetics 167, 523–530 (2004).
  Article PubMed PubMed Central Google Scholar
• Newman, J. R. S. et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840–846 (2006).
  Article CAS PubMed Google Scholar
• Chambers, I. et al. Nanog safeguards pluripotency and mediates germline development. Nature 450, 1230–1234 (2007). This study shows that NANOG expression fluctuates in ES cells and that it provides a temporary predisposition towards cell differentiation.
  Article CAS PubMed Google Scholar
• Feng, B. et al. Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nature Cell Biol. 11, 197–203 (2009).
  Article CAS PubMed Google Scholar
• Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917–1920 (2007).
  Article CAS PubMed Google Scholar
• Nakagawa, M. et al. Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nature Biotechnol. 26, 101–106 (2008).
  Article CAS Google Scholar
• Wernig, M., Meissner, A., Cassady, J. P. & Jaenisch, R. c-Myc is dispensable for direct reprogramming of mouse fibroblasts. Cell Stem Cell 2, 10–12 (2008).
  Article CAS PubMed Google Scholar
• Aoi, T. et al. Generation of pluripotent stem cells from adult mouse liver and stomach cells. Science 321, 699–702 (2008).
  Article CAS PubMed Google Scholar
• Park, I.-H. et al. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451, 141–146 (2008).
  Article CAS PubMed Google Scholar
• Kim, J. B. et al. Oct4-induced pluripotency in adult neural stem cells. Cell 136, 411–419 (2009).
  Article CAS PubMed Google Scholar
• Maherali, N. et al. directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell 1, 55–70 (2007).
  CAS Google Scholar
• Okita, K., Ichisaka, T. & Yamanaka, S. Generation of germline-competent induced pluripotent stem cells. Nature 448, 313–317 (2007).
  Article CAS PubMed Google Scholar
• Wernig, M. et al. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature 448, 318–324 (2007).
  Article CAS PubMed Google Scholar
• Sridharan, R. et al. Role of the murine reprogramming factors in the induction of pluripotency. Cell 136, 364–377 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49–55 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Jaenisch, R. & Young, R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132, 567–582 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Hemberger, M., Dean, W. & Reik, W. Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington's canal. Nature Rev. Mol. Cell Biol. 10, 526–537 (2009).
  Article CAS Google Scholar
• Ivanova, N. et al. Dissecting self-renewal in stem cells with RNA interference. Nature 442, 533–538 (2006).
  Article CAS PubMed Google Scholar
• Daheron, L. et al. LIF/STAT3 signaling fails to maintain self-renewal of human embryonic stem cells. Stem Cells 22, 770–778 (2004).
  Article CAS PubMed Google Scholar
• Nishimoto, M., Fukushima, A., Okuda, A. & Muramatsu, M. The gene for the embryonic stem cell coactivator UTF1 carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2. Mol. Cell. Biol. 19, 5453–5465 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Yuan, H., Corbi, N., Basilico, C. & Dailey, L. Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3. Genes Dev. 9, 2635–2645 (1995).
  Article CAS PubMed Google Scholar
• Zhang, P. et al. Negative cross-talk between hematopoietic regulators: GATA proteins repress PU.1. Proc. Natl Acad. Sci. USA 96, 8705–8710 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• van den Berg, D. L. C. et al. Estrogen-related receptor β interacts with Oct4 To positively regulate Nanog gene expression. Mol. Cell. Biol. 28, 5986–5995 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, X., Zhang, J., Wang, T., Esteban, M. A. & Pei, D. Esrrb activates Oct4 transcription and sustains self-renewal and pluripotency in embryonic stem cells. J. Biol. Chem. 283, 35825–35833 (2008).
  Article CAS PubMed Google Scholar