The transcriptional and signalling networks of pluripotency (original) (raw)
Evans, M. J. & Kaufman, M. H. Establishment in culture of pluripotential cells from mouse embryos. Nature292, 154–156 (1981). CASPubMed Google Scholar
Martin, G. R. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl Acad. Sci. USA78, 7634–7638 (1981). CASPubMedPubMed Central Google Scholar
Smith, A. G. et al. Inhibition of pluripotential embryonic stem cell differentiation by purified polypeptides. Nature336, 688–690 (1988). CASPubMed Google Scholar
Williams, R. L. et al. Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells. Nature336, 684–687 (1988). CASPubMed Google Scholar
Ying, Q. L., Nichols, J., Chambers, I. & Smith, A. BMP induction of Id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3. Cell115, 281–292 (2003). CASPubMed Google Scholar
Niwa, H., Burdon, T., Chambers, I. & Smith, A. Self-renewal of pluripotent embryonic stem cells is mediated via activation of STAT3. Genes Dev.12, 2048–2060 (1998). CASPubMedPubMed Central Google Scholar
Thomson, J. A. et al. Embryonic stem cell lines derived from human blastocysts. Science282, 1145–1147 (1998). ArticleCASPubMed Google Scholar
Reubinoff, B. E., Pera, M. F., Fong, C. Y., Trounson, A. & Bongso, A. Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro. Nat. Biotechnol.18, 399–404 (2000). CASPubMed Google Scholar
Armstrong, L. et al. The role of PI3K/AKT, MAPK/ERK and NFκβ signalling in the maintenance of human embryonic stem cell pluripotency and viability highlighted by transcriptional profiling and functional analysis. Hum. Mol. Genet.15, 1894–1913 (2006). CASPubMed Google Scholar
Li, J. et al. MEK/ERK signalling contributes to the maintenance of human embryonic stem cell self-renewal. Differentiation75, 299–307 (2007). CASPubMed Google Scholar
Vallier, L., Reynolds, D. & Pedersen, R. A. Nodal inhibits differentiation of human embryonic stem cells along the neuroectodermal default pathway. Dev. Biol.275, 403–421 (2004). CASPubMed Google Scholar
Xu, R. H. et al. Basic FGF and suppression of BMP signalling sustain undifferentiated proliferation of human ES cells. Nat. Methods2, 185–190 (2005). CASPubMed Google Scholar
Beattie, G. M. et al. Activin A maintains pluripotency of human embryonic stem cells in the absence of feeder layers. Stem Cells23, 489–495 (2005). CASPubMed Google Scholar
James, D., Levine, A. J., Besser, D. & Hemmati-Brivanlou, A. TGFβ/activin/nodal signalling is necessary for the maintenance of pluripotency in human embryonic stem cells. Development132, 1273–1282 (2005). CASPubMed Google Scholar
Vallier, L., Alexander, M. & Pedersen, R. A. Activin/Nodal and FGF pathways cooperate to maintain pluripotency of human embryonic stem cells. J. Cell Sci.118, 4495–4509 (2005). CASPubMed Google Scholar
Niwa, H., Miyazaki, J. & Smith, A. G. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat. Genet.24, 372–376 (2000). CASPubMed Google Scholar
Masui, S. et al. Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nat. Cell. Biol.9, 625–635 (2007). CASPubMed Google Scholar
Boiani, M. & Schöler, H. R. Regulatory networks in embryo-derived pluripotent stem cells. Nat. Rev. Mol. Cell Biol.6, 872–884 (2005). CASPubMed Google Scholar
Chambers, I. et al. Nanog safeguards pluripotency and mediates germline development. Nature450, 1230–1234 (2007). CASPubMed Google Scholar
Chambers, I. et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell113, 643–655 (2003). CASPubMed Google Scholar
Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell122, 947–956 (2005). CASPubMedPubMed Central Google Scholar
Loh, Y. H. et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet.38, 431–440 (2006). CASPubMed Google Scholar
Chen, X. et al. Integration of external signalling pathways with the core transcriptional network in embryonic stem cells. Cell133, 1106–1117 (2008). ArticleCASPubMed Google Scholar
Kim, J., Chu, J., Shen, X., Wang, J. & Orkin, S. H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell132, 1049–1061 (2008). CASPubMed Google Scholar
Cole, M. F., Johnstone, S. E., Newman, J. J., Kagey, M. H. & Young, R. A. Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev.22, 746–755 (2008). CASPubMedPubMed Central Google Scholar
Feng, B. et al. Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nat. Cell Biol.11, 197–203 (2009). CASPubMed Google Scholar
Heng, J. C. et al. The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. Cell Stem Cell6, 167–174 (2010). CASPubMed Google Scholar
Dejosez, M. et al. Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells. Genes Dev.24, 1479–1484 (2010). CASPubMedPubMed Central Google Scholar
Wang, J. et al. A protein interaction network for pluripotency of embryonic stem cells. Nature444, 364–368 (2006). CASPubMed Google Scholar
van den Berg, D. L. et al. An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell6, 369–381 (2010). CASPubMedPubMed Central Google Scholar
Kim, J. et al. A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell143, 313–324 (2010). CASPubMedPubMed Central Google Scholar
Lim, C. Y. et al. Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages. Cell Stem Cell3, 543–554 (2008). CASPubMed Google Scholar
Jiang, J. et al. A core Klf circuitry regulates self-renewal of embryonic stem cells. Nat. Cell Biol.10, 353–360 (2008). PubMed Google Scholar
Chew, J. L. et al. Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells. Mol. Cell Biol.25, 6031–6046 (2005). ArticleCASPubMedPubMed Central Google Scholar
Mitsui, K. et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell113, 631–642 (2003). CASPubMed Google Scholar
Zhang, J. et al. Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1. Nat. Cell Biol.8, 1114–1123 (2006). CASPubMed Google Scholar
Chambers, I. & Tomlinson, S. R. The transcriptional foundation of pluripotency. Development136, 2311–2322 (2009). CASPubMedPubMed Central Google Scholar
Ouyang, Z., Zhou, Q. & Wong, W. H. ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc. Natl Acad. Sci. USA106, 21521–21526 (2009). CASPubMedPubMed Central Google Scholar
Sharov, A. A. et al. Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data. BMC Genomics9, 269 (2008). PubMedPubMed Central Google Scholar
Loh, Y. H., Zhang, W., Chen, X., George, J. & Ng, H-H. Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev.21, 2545–2557 (2007). CASPubMedPubMed Central Google Scholar
Walker, E. et al. Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation. Cell Stem Cell6, 153–166 (2010). CASPubMedPubMed Central Google Scholar
Landeira, D. et al. Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators. Nat. Cell Biol.12, 618–624 (2010). CASPubMedPubMed Central Google Scholar
Pasini, D. et al. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature464, 306–310 (2010). CASPubMed Google Scholar
Shen, X. et al. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell139, 1303–1314 (2009). PubMedPubMed Central Google Scholar
Peng, J. C. et al. Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell139, 1290–1302 (2009). PubMedPubMed Central Google Scholar
Meshorer, E. & Misteli, T. Chromatin in pluripotent embryonic stem cells and differentiation. Nat. Rev. Mol. Cell Biol.7, 540–546 (2006). CASPubMed Google Scholar
Marson, A. et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell134, 521–533 (2008). ArticleCASPubMedPubMed Central Google Scholar
Wang, Y. et al. Embryonic stem cell-specific microRNAs regulate the G1–S transition and promote rapid proliferation. Nat. Genet.40, 1478–1483 (2008). CASPubMedPubMed Central Google Scholar
Lichner, Z. et al. The miR-290–295 cluster promotes pluripotency maintenance by regulating cell cycle phase distribution in mouse embryonic stem cells. Differentiation81, 11–24 (2010). PubMed Google Scholar
Melton, C., Judson, R. L. & Blelloch, R. Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature463, 621–626 (2010). CASPubMedPubMed Central Google Scholar
Viswanathan, S. R., Daley, G. Q. & Gregory, R. I. Selective blockade of microRNA processing by Lin28. Science320, 97–100 (2008). CASPubMedPubMed Central Google Scholar
Rosa, A., Spagnoli, F. M. & Brivanlou, A. H. The miR-430/427/302 family controls mesendodermal fate specification via species-specific target selection. Dev. Cell16, 517–527 (2009). CASPubMed Google Scholar
Navarro, P. et al. Molecular coupling of Xist regulation and pluripotency. Science321, 1693–1695 (2008). CASPubMed Google Scholar
Loewer, S. et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat. Genet.42, 1113–1117 (2010). CASPubMedPubMed Central Google Scholar
Ivanova, N. et al. Dissecting self-renewal in stem cells with RNA interference. Nature442, 533–538 (2006). CASPubMed Google Scholar
Fazzio, T. G., Huff, J. T. & Panning, B. An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identity. Cell134, 162–174 (2008). CASPubMedPubMed Central 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 Cell4, 403–415 (2009). CASPubMed 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). CASPubMedPubMed Central Google Scholar
Kagey, M. H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature467, 430–435 (2010). CASPubMedPubMed Central Google Scholar
Xiong, B. & Gerton, J. L. Regulators of the cohesin network. Annu. Rev. Biochem.79, 131–153 (2010). CASPubMed Google Scholar
Chia, N. Y. et al. A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature468, 316–320 (2010). CASPubMed Google Scholar
Subramanian, V., Klattenhoff, C. A. & Boyer, L. A. Screening for novel regulators of embryonic stem cell identity. Cell Stem Cell4, 377–378 (2009). CASPubMed Google Scholar
Yamaji, M. et al. Critical function of Prdm14 for the establishment of the germ cell lineage in mice. Nat. Genet.40, 1016–1022 (2008). CASPubMed Google Scholar
Tsuneyoshi, N. et al. PRDM14 suppresses expression of differentiation marker genes in human embryonic stem cells. Biochem. Biophys. Res. Commun.367, 899–905 (2008). CASPubMed Google Scholar
Ma, Z., Swigut, T., Valouev, A., Rada-Iglesias, A. & Wysocka, J. Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates. Nat. Struct. Mol. Biol.18, 120–127 (2011). CASPubMed Google Scholar
Kunarso, G. et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet.42, 631–634 (2010). CASPubMed Google Scholar
Bourque, G. et al. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res.18, 1752–1762 (2008). CASPubMedPubMed Central Google Scholar
Kunath, T. et al. FGF stimulation of the Erk1/2 signalling cascade triggers transition of pluripotent embryonic stem cells from self-renewal to lineage commitment. Development134, 2895–2902 (2007). CASPubMed Google Scholar
Nichols, J. & Smith, A. Naive and primed pluripotent states. Cell Stem Cell4, 487–492 (2009). CASPubMed Google Scholar
Brons, I. G. et al. Derivation of pluripotent epiblast stem cells from mammalian embryos. Nature448, 191–195 (2007). CASPubMed Google Scholar
Tesar, P. J. et al. New cell lines from mouse epiblast share defining features with human embryonic stem cells. Nature448, 196–199 (2007). CASPubMed Google Scholar
Bao, S. et al. Epigenetic reversion of post-implantation epiblast to pluripotent embryonic stem cells. Nature461, 1292–1295 (2009). CASPubMed Google Scholar
Leitch, H. G. et al. Embryonic germ cells from mice and rats exhibit properties consistent with a generic pluripotent ground state. Development137, 2279–2287 (2010). CASPubMedPubMed Central Google Scholar
Xu, R. H. et al. NANOG is a direct target of TGFβ/activin-mediated SMAD signalling in human ESCs. Cell Stem Cell3, 196–206 (2008). CASPubMedPubMed Central Google Scholar
Greber, B. et al. Conserved and divergent roles of FGF signalling in mouse epiblast stem cells and human embryonic stem cells. Cell Stem Cell6, 215–226 (2010). CASPubMed Google Scholar
Vallier, L. et al. Activin/Nodal signalling maintains pluripotency by controlling Nanog expression. Development136, 1339–1349 (2009). CASPubMedPubMed Central Google Scholar
Guo, G. & Smith, A. A genome-wide screen in EpiSCs identifies Nr5a nuclear receptors as potent inducers of ground state pluripotency. Development137, 3185–3192 (2010). CASPubMedPubMed Central Google Scholar
Guo, G. et al. Klf4 reverts developmentally programmed restriction of ground state pluripotency. Development136, 1063–1069 (2009). CASPubMedPubMed Central Google Scholar
Hall, J. et al. Oct4 and LIF/Stat3 additively induce Kruppel factors to sustain embryonic stem cell self-renewal. Cell Stem Cell5, 597–609 (2009). CASPubMed Google Scholar
Yang, J. et al. Stat3 activation is limiting for reprogramming to ground state pluripotency. Cell Stem Cell7, 319–328 (2010). CASPubMedPubMed Central Google Scholar
Hayashi, K., Lopes, S. M., Tang, F. & Surani, M. A. Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states. Cell Stem Cell3, 391–401 (2008). CASPubMed Google Scholar
Han, D. W. et al. Epiblast stem cell subpopulations represent mouse embryos of distinct pregastrulation stages. Cell143, 617–627 (2010). CASPubMed Google Scholar
Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell131, 861–872 (2007). CASPubMed Google Scholar
Park, I. H. et al. Reprogramming of human somatic cells to pluripotency with defined factors. Nature451, 141–146 (2008). CASPubMed Google Scholar
Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science318, 1917–1920 (2007). CASPubMed Google Scholar
Li, W. et al. Generation of rat and human induced pluripotent stem cells by combining genetic reprogramming and chemical inhibitors. Cell Stem Cell4, 16–19 (2009). PubMed Google Scholar
Chambers, S. M. et al. Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signalling. Nat. Biotechnol.27, 275–280 (2009). CASPubMedPubMed Central Google Scholar
Buecker, C. et al. A murine ESC-like state facilitates transgenesis and homologous recombination in human pluripotent stem cells. Cell Stem Cell6, 535–546 (2010). CASPubMedPubMed Central Google Scholar
Hanna, J. et al. Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs. Proc. Natl Acad. Sci. USA107, 9222–9227 (2010). CASPubMedPubMed Central Google Scholar
Xu, Y. et al. Revealing a core signalling regulatory mechanism for pluripotent stem cell survival and self-renewal by small molecules. Proc. Natl Acad. Sci. USA107, 8129–8134 (2010). CASPubMedPubMed Central Google Scholar