Abstract
Pluripotency is a defining feature of embryonic stem cells (ESCs). A mechanistic understanding of pluripotency should shed light on fundamental aspects of development. In this chapter, we review the extrinsic factors, protein, and gene regulatory networks and epigenetics of ESCs. With the availability of human ESCs and the capacity to reprogram somatic cells to a pluripotent state, we hope that a comprehensive description of the control of pluripotency in ESCs will contribute to the use of these cells in regenerative medicine.
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Ananiev, G.E., Goldstein, S., Runnheim, R., Forrest, D.K., Zhou, S., Potamousis, K., Churas, C.P., Bergendahl, V., Thomson, J.A., Schwartz, D.C., 2008. Optical mapping discerns genome wide DNA methylation profiles. BMC Mol Biol 9, 68.
Avery, K., Avery, S., Shepherd, J., Heath, P.R., Moore, H., 2008. Sphingosine-1-phosphate mediates transcriptional regulation of key targets associated with survival, proliferation and pluripotency in human embryonic stem cells. Stem Cells Dev 17(6), 1995–1205.
Avilion, A.A., Nicolis, S.K., Pevny, L.H., Perez, L., Vivian, N., Lovell-Badge, R., 2003. Multipotent cell lineages in early mouse development depend on SOX2 function. Genes Dev 17, 126–140.
Babaie, Y., Herwig, R., Greber, B., Brink, T.C., Wruck, W., Groth, D., Lehrach, H., Burdon, T., Adjaye, J., 2007. Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells. Stem Cells 25, 500–510.
Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., Zhao, K., 2007. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837.
Beattie, G.M., Lopez, A.D., Bucay, N., Hinton, A., Firpo, M.T., King, C.C., Hayek, A., 2005. Activin A maintains pluripotency of human embryonic stem cells in the absence of feeder layers. Stem Cells 23, 489–495.
Beppu, H., Kawabata, M., Hamamoto, T., Chytil, A., Minowa, O., Noda, T., Miyazono, K., 2000. BMP type II receptor is required for gastrulation and early development of mouse embryos. Dev Biol 221, 249–258.
Bernstein, B.E., Kamal, M., Lindblad-Toh, K., Bekiranov, S., Bailey, D.K., Huebert, D.J., McMahon, S., Karlsson, E.K., Kulbokas, E.J., 3rd, Gingeras, T.R., Schreiber, S.L., Lander, E.S., 2005. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169–181.
Bernstein, B.E., Mikkelsen, T.S., Xie, X., Kamal, M., Huebert, D.J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., Jaenisch, R., Wagschal, A., Feil, R., Schreiber, S.L., Lander, E.S., 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326.
Boguski, M.S., Lowe, T.M., Tolstoshev, C.M., 1993. dbEST-database for “expressed sequence tags”. Nat Genet 4, 332–333.
Boheler, K.R., Tarasov, K.V., 2006. SAGE analysis to identify embryonic stem cell-predominant transcripts. Methods Mol Biol 329, 195-221.
Boyer, L.A., Lee, T.I., Cole, M.F., Johnstone, S.E., Levine, S.S., Zucker, J.P., Guenther, M.G., Kumar, R.M., Murray, H.L., Jenner, R.G., Gifford, D.K., Melton, D.A., Jaenisch, R., Young, R.A., 2005. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956.
Boyer, L.A., Mathur, D., Jaenisch, R., 2006a. Molecular control of pluripotency. Curr Opin Genet Dev 16, 455–462.
Boyer, L.A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L.A., Lee, T.I., Levine, S.S., Wernig, M., Tajonar, A., Ray, M.K., Bell, G.W., Otte, A.P., Vidal, M., Gifford, D.K., Young, R.A., Jaenisch, R., 2006b. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349–353.
Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., Roth, R., George, D., Eletr, S., Albrecht, G., Vermaas, E., Williams, S.R., Moon, K., Burcham, T., Pallas, M., DuBridge, R.B., Kirchner, J., Fearon, K., Mao, J., Corcoran, K., 2000. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18, 630–634.
Buck, M.J., Lieb, J.D., 2004. ChIP-ChIP: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83, 349–360.
Burdon, T., Stracey, C., Chambers, I., Nichols, J., Smith, A., 1999. Suppression of SHP-2 and ERK signalling promotes self-renewal of mouse embryonic stem cells. Dev Biol 210, 30–43.
Cao, R., Wang, L., Wang, H., Xia, L., Erdjument-Bromage, H., Tempst, P., Jones, R.S., Zhang, Y., 2002. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043.
Cartwright, P., McLean, C., Sheppard, A., Rivett, D., Jones, K., Dalton, S., 2005. LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent mechanism. Development 132, 885–896.
Chamberlain, S.J., Yee, D., Magnuson, T., 2008. Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency. Stem Cells 26, 1496-1505.
Chambers, I., Colby, D., Robertson, M., Nichols, J., Lee, S., Tweedie, S., Smith, A., 2003. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 113, 643–655.
Chambers, I., Silva, J., Colby, D., Nichols, J., Nijmeijer, B., Robertson, M., Vrana, J., Jones, K., Grotewold, L., Smith, A., 2007. Nanog safeguards pluripotency and mediates germline development. Nature 450, 1230–1234.
Chazaud, C., Yamanaka, Y., Pawson, T., Rossant, J., 2006. Early lineage segregation between epiblast and primitive endoderm in mouse blastocysts through the Grb2-MAPK pathway. Dev Cell 10, 615–624.
Chen, D., Zhao, M., Mundy, G.R., 2004. Bone morphogenetic proteins. Growth Factors 22, 233–241.
Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V.B., Wong, E., Orlov, Y.L., Zhang, W., Jiang, J., Loh, Y.H., Yeo, H.C., Yeo, Z.X., Narang, V., Govindarajan, K.R., Leong, B., Shahab, A., Ruan, Y., Bourque, G., Sung, W.K., Clarke, N.D., Wei, C.L., Ng, H.H., 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106–1117.
Cheng, L., Sung, M.T., Cossu-Rocca, P., Jones, T.D., MacLennan, G.T., De Jong, J., Lopez-Beltran, A., Montironi, R., Looijenga, L.H., 2007. OCT4: biological functions and clinical applications as a marker of germ cell neoplasia. J Pathol 211, 1–9.
Chew, J.L., Loh, Y.H., Zhang, W., Chen, X., Tam, W.L., Yeap, L.S., Li, P., Ang, Y.S., Lim, B., Robson, P., Ng, H.H., 2005. Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells. Mol Cell Biol 25, 6031–6046.
Christensen, J., Agger, K., Cloos, P.A., Pasini, D., Rose, S., Sennels, L., Rappsilber, J., Hansen, K.H., Salcini, A.E., Helin, K., 2007. RBP2 belongs to a family of demethylases, specific for tri- and dimethylated lysine 4 on histone 3. Cell 128, 1063–1076.
Cole, M.F., Johnstone, S.E., Newman, J.J., Kagey, M.H., Young, R.A., 2008. Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev 22, 746–755.
Daheron, L., Opitz, S.L., Zaehres, H., Lensch, M.W., Andrews, P.W., Itskovitz-Eldor, J., Daley, G.Q., 2004. LIF/STAT3 signaling fails to maintain self-renewal of human embryonic stem cells. Stem Cells 22, 770–778.
Elling, U., Klasen, C., Eisenberger, T., Anlag, K., Treier, M., 2006. Murine inner cell mass-derived lineages depend on Sall4 function. Proc Natl Acad Sci U S A 103, 16319–16324.
Elliott, S.T., Crider, D.G., Garnham, C.P., Boheler, K.R., Van Eyk, J.E., 2004. Two-dimensional gel electrophoresis database of murine R1 embryonic stem cells. Proteomics 4, 3813–3832.
Endoh, M., Endo, T.A., Endoh, T., Fujimura, Y., Ohara, O., Toyoda, T., Otte, A.P., Okano, M., Brockdorff, N., Vidal, M., Koseki, H., 2008. Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity. Development 135, 1513–1524.
Euskirchen, G.M., Rozowsky, J.S., Wei, C.L., Lee, W.H., Zhang, Z.D., Hartman, S., Emanuelsson, O., Stolc, V., Weissman, S., Gerstein, M.B., Ruan, Y., Snyder, M., 2007. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res 17, 898–909.
Evans, M.J., Kaufman, M.H., 1981. Establishment in culture of pluripotential cells from mouse embryos. Nature 292, 154–156.
Faust, C., Lawson, K.A., Schork, N.J., Thiel, B., Magnuson, T., 1998. The Polycomb-group gene eed is required for normal morphogenetic movements during gastrulation in the mouse embryo. Development 125, 4495–4506.
Foshay, K.M., Gallicano, G.I., 2007. Small RNAs, big potential: the role of MicroRNAs in stem cell function. Curr Stem Cell Res Ther 2, 264–271.
Francis, N.J., Kingston, R.E., 2001. Mechanisms of transcriptional memory. Nat Rev Mol Cell Biol 2, 409–421.
Fujikura, J., Yamato, E., Yonemura, S., Hosoda, K., Masui, S., Nakao, K., Miyazaki Ji, J., Niwa, H., 2002. Differentiation of embryonic stem cells is induced by GATA factors. Genes Dev 16, 784–789.
Gan, Q., Yoshida, T., McDonald, O.G., Owens, G.K., 2007. Concise review: epigenetic mechanisms contribute to pluripotency and cell lineage determination of embryonic stem cells. Stem Cells 25, 2–9.
Gasca, S., Canizares, J., De Santa Barbara, P., Mejean, C., Poulat, F., Berta, P., Boizet-Bonhoure, B., 2002. A nuclear export signal within the high mobility group domain regulates the nucleocytoplasmic translocation of SOX9 during sexual determination. Proc Natl Acad Sci U S A 99, 11199–11204.
Gitan, R.S., Shi, H., Chen, C.M., Yan, P.S., Huang, T.H., 2002. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res 12, 158–164.
Gough, N.M., Gearing, D.P., King, J.A., Willson, T.A., Hilton, D.J., Nicola, N.A., Metcalf, D., 1988. Molecular cloning and expression of the human homologue of the murine gene encoding myeloid leukemia-inhibitory factor. Proc Natl Acad Sci U S A 85, 2623–2627.
Greber, B., Lehrach, H., Adjaye, J., 2007a. Fibroblast growth factor 2 modulates transforming growth factor beta signaling in mouse embryonic fibroblasts and human ESCs (hESCs) to support hESC self-renewal. Stem Cells 25, 455–464.
Greber, B., Lehrach, H., Adjaye, J., 2007b. Silencing of core transcription factors in human EC cells highlights the importance of autocrine FGF signaling for self-renewal. BMC Dev Biol 7, 46.
Guenther, M.G., Levine, S.S., Boyer, L.A., Jaenisch, R., Young, R.A., 2007. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88.
Hao, J., Li, T.G., Qi, X., Zhao, D.F., Zhao, G.Q., 2006. WNT/beta-catenin pathway up-regulates Stat3 and converges on LIF to prevent differentiation of mouse embryonic stem cells. Dev Biol 290, 81–91.
Hatfield, S.D., Shcherbata, H.R., Fischer, K.A., Nakahara, K., Carthew, R.W., Ruohola-Baker, H., 2005. Stem cell division is regulated by the microRNA pathway. Nature 435, 974–978.
Herr, W., Cleary, M.A., 1995. The POU domain: versatility in transcriptional regulation by a flexible two-in-one DNA-binding domain. Genes Dev 9, 1679–1693.
Hollnagel, A., Oehlmann, V., Heymer, J., Ruther, U., Nordheim, A., 1999. Id genes are direct targets of bone morphogenetic protein induction in embryonic stem cells. J Biol Chem 274, 19838–19845.
Hong, S., Cho, Y.W., Yu, L.R., Yu, H., Veenstra, T.D., Ge, K., 2007. Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. Proc Natl Acad Sci U S A 104, 18439–18444.
Ikegami, K., Iwatani, M., Suzuki, M., Tachibana, M., Shinkai, Y., Tanaka, S., Greally, J.M., Yagi, S., Hattori, N., Shiota, K., 2007. Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cells. Genes Cells 12, 1–11.
Ivanova, N., Dobrin, R., Lu, R., Kotenko, I., Levorse, J., DeCoste, C., Schafer, X., Lun, Y., Lemischka, I.R., 2006. Dissecting self-renewal in stem cells with RNA interference. Nature 442, 533–538.
James, D., Levine, A.J., Besser, D., Hemmati-Brivanlou, A., 2005. TGFbeta/activin/nodal signaling is necessary for the maintenance of pluripotency in human embryonic stem cells. Development 132, 1273–1282.
Johnson, D.S., Mortazavi, A., Myers, R.M., Wold, B., 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502.
Kaji, K., Nichols, J., Hendrich, B., 2007. Mbd3, a component of the NuRD co-repressor complex, is required for development of pluripotent cells. Development 134, 1123–1132.
Kanellopoulou, C., Muljo, S.A., Kung, A.L., Ganesan, S., Drapkin, R., Jenuwein, T., Livingston, D.M., Rajewsky, K., 2005. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19, 489–501.
Keller, G., 2005. Embryonic stem cell differentiation: emergence of a new era in biology and medicine. Genes Dev 19, 1129–1155.
Kim, J., Chu, J., Shen, X., Wang, J., Orkin, S.H., 2008. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049–1061.
Kim, T.H., Barrera, L.O., Zheng, M., Qu, C., Singer, M.A., Richmond, T.A., Wu, Y., Green, R.D., Ren, B., 2005. A high-resolution map of active promoters in the human genome. Nature 436, 876–880.
Kleinsmith, L.J., Pierce, G.B., Jr., 1964. Multipotentiality of Single Embryonal Carcinoma Cells. Cancer Res 24, 1544–1551.
Kuroda, T., Tada, M., Kubota, H., Kimura, H., Hatano, S.Y., Suemori, H., Nakatsuji, N., Tada, T., 2005. Octamer and Sox elements are required for transcriptional cis regulation of Nanog gene expression. Mol Cell Biol 25, 2475–2485.
Lengner, C.J., Camargo, F.D., Hochedlinger, K., Welstead, G.G., Zaidi, S., Gokhale, S., Scholer, H.R., Tomilin, A., Jaenisch, R., 2007. Oct4 expression is not required for mouse somatic stem cell self-renewal. Cell Stem Cell 1, 403–415.
Levine, S.S., Weiss, A., Erdjument-Bromage, H., Shao, Z., Tempst, P., Kingston, R.E., 2002. The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans. Mol Cell Biol 22, 6070–6078.
Li, B., Carey, M., Workman, J.L., 2007a. The role of chromatin during transcription. Cell 128, 707–719.
Li, J., Pan, G., Cui, K., Liu, Y., Xu, S., Pei, D., 2007b. A dominant-negative form of mouse SOX2 induces trophectoderm differentiation and progressive polyploidy in mouse embryonic stem cells. J Biol Chem 282, 19481–19492.
Li, J., Wang, G., Wang, C., Zhao, Y., Zhang, H., Tan, Z., Song, Z., Ding, M., Deng, H., 2007c. MEK/ERK signaling contributes to the maintenance of human embryonic stem cell self-renewal. Differentiation 75, 299–307.
Li, M., Sendtner, M., Smith, A., 1995. Essential function of LIF receptor in motor neurons. Nature 378, 724–727.
Liedtke, S., Enczmann, J., Waclawczyk, S., Wernet, P., Kogler, G., 2007. Oct4 and its pseudogenes confuse stem cell research. Cell Stem Cell 1, 364–366.
Loh, Y.H., Wu, Q., Chew, J.L., Vega, V.B., Zhang, W., Chen, X., Bourque, G., George, J., Leong, B., Liu, J., Wong, K.Y., Sung, K.W., Lee, C.W., Zhao, X.D., Chiu, K.P., Lipovich, L., Kuznetsov, V.A., Robson, P., Stanton, L.W., Wei, C.L., Ruan, Y., Lim, B., Ng, H.H., 2006. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 38, 431–440.
Loh, Y.H., Zhang, W., Chen, X., George, J., Ng, H.H., 2007. Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev 21, 2545–2557.
Marson, A., Levine, S.S., Cole, M.F., Frampton, G.M., Brambrink, T., Johnstone, S., Guenther, M.G., Johnston, W.K., Wernig, M., Newman, J., Calabrese, J.M., Dennis, L.M., Volkert, T.L., Gupta, S., Love, J., Hannett, N., Sharp, P.A., Bartel, D.P., Jaenisch, R., Young, R.A., 2008. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521–533.
Martin, G.R., 1981. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc Natl Acad Sci U S A 78, 7634–7638.
Maruyama, M., Ichisaka, T., Nakagawa, M., Yamanaka, S., 2005. Differential roles for Sox15 and Sox2 in transcriptional control in mouse embryonic stem cells. J Biol Chem 280, 24371–24379.
Masui, S., Nakatake, Y., Toyooka, Y., Shimosato, D., Yagi, R., Takahashi, K., Okochi, H., Okuda, A., Matoba, R., Sharov, A.A., Ko, M.S., Niwa, H., 2007. Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nat Cell Biol 9, 625–635.
Mathur, D., Danford, T.W., Boyer, L.A., Young, R.A., Gifford, D.K., Jaenisch, R., 2008. Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-ChIP and ChIP-PET. Genome Biol 9, R126.
Matsuda, T., Nakamura, T., Nakao, K., Arai, T., Katsuki, M., Heike, T., Yokota, T., 1999. STAT3 activation is sufficient to maintain an undifferentiated state of mouse embryonic stem cells. Embo J 18, 4261–4269.
Mendenhall, E.M., Bernstein, B.E., 2008. Chromatin state maps: new technologies, new insights. Curr Opin Genet Dev 18, 109–115.
Metzger, E., Wissmann, M., Yin, N., Muller, J.M., Schneider, R., Peters, A.H., Gunther, T., Buettner, R., Schule, R., 2005. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 437, 436–439.
Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.K., Koche, R.P., Lee, W., Mendenhall, E., O'Donovan, A., Presser, A., Russ, C., Xie, X., Meissner, A., Wernig, M., Jaenisch, R., Nusbaum, C., Lander, E.S., Bernstein, B.E., 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560.
Mishina, Y., Suzuki, A., Ueno, N., Behringer, R.R., 1995. Bmpr encodes a type I bone morphogenetic protein receptor that is essential for gastrulation during mouse embryogenesis. Genes Dev 9, 3027–3037.
Mitsui, K., Tokuzawa, Y., Itoh, H., Segawa, K., Murakami, M., Takahashi, K., Maruyama, M., Maeda, M., Yamanaka, S., 2003. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113, 631–642.
Miyagi, S., Masui, S., Niwa, H., Saito, T., Shimazaki, T., Okano, H., Nishimoto, M., Muramatsu, M., Iwama, A., Okuda, A., 2008. Consequence of the loss of Sox2 in the developing brain of the mouse. FEBS Lett 582, 2811–2815.
Morin-Kensicki, E.M., Faust, C., LaMantia, C., Magnuson, T., 2001. Cell and tissue requirements for the gene eed during mouse gastrulation and organogenesis. Genesis 31, 142–146.
Murchison, E.P., Partridge, J.F., Tam, O.H., Cheloufi, S., Hannon, G.J., 2005. Characterization of Dicer-deficient murine embryonic stem cells. Proc Natl Acad Sci U S A 102, 12135–12140.
Nagano, K., Taoka, M., Yamauchi, Y., Itagaki, C., Shinkawa, T., Nunomura, K., Okamura, N., Takahashi, N., Izumi, T., Isobe, T., 2005. Large-scale identification of proteins expressed in mouse embryonic stem cells. Proteomics 5, 1346–1361.
Nakatake, Y., Fukui, N., Iwamatsu, Y., Masui, S., Takahashi, K., Yagi, R., Yagi, K., Miyazaki, J., Matoba, R., Ko, M.S., Niwa, H., 2006. Klf4 cooperates with Oct3/4 and Sox2 to activate the Lefty1 core promoter in embryonic stem cells. Mol Cell Biol 26, 7772–7782.
Nakayama, K., Tamura, Y., Suzawa, M., Harada, S., Fukumoto, S., Kato, M., Miyazono, K., Rodan, G.A., Takeuchi, Y., Fujita, T., 2003. Receptor tyrosine kinases inhibit bone morphogenetic protein-Smad responsive promoter activity and differentiation of murine MC3T3-E1 osteoblast-like cells. J Bone Miner Res 18, 827–835.
Ng, R.K., Gurdon, J.B., 2008. Epigenetic inheritance of cell differentiation status. Cell Cycle 7, 1173–1177.
Niakan, K.K., Davis, E.C., Clipsham, R.C., Jiang, M., Dehart, D.B., Sulik, K.K., McCabe, E.R., 2006. Novel role for the orphan nuclear receptor Dax1 in embryogenesis, different from steroidogenesis. Mol Genet Metab 88, 261–271.
Nichols, J., Zevnik, B., Anastassiadis, K., Niwa, H., Klewe-Nebenius, D., Chambers, I., Scholer, H., Smith, A., 1998. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95, 379–391.
Nishimoto, M., Fukushima, A., Miyagi, S., Suzuki, Y., Sugano, S., Matsuda, Y., Hori, T., Muramatsu, M., Okuda, A., 2001. Structural analyses of the UTF1 gene encoding a transcriptional coactivator expressed in pluripotent embryonic stem cells. Biochem Biophys Res Commun 285, 945–953.
Niwa, H., Burdon, T., Chambers, I., Smith, A., 1998. Self-renewal of pluripotent embryonic stem cells is mediated via activation of STAT3. Genes Dev 12, 2048–2060.
Niwa, H., Miyazaki, J., Smith, A.G., 2000. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet 24, 372–376.
Niwa, H., Toyooka, Y., Shimosato, D., Strumpf, D., Takahashi, K., Yagi, R., Rossant, J., 2005. Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation. Cell 123, 917–929.
O'Carroll, D., Erhardt, S., Pagani, M., Barton, S.C., Surani, M.A., Jenuwein, T., 2001. The polycomb-group gene Ezh2 is required for early mouse development. Mol Cell Biol 21, 4330–4336.
Ogawa, K., Nishinakamura, R., Iwamatsu, Y., Shimosato, D., Niwa, H., 2006. Synergistic action of Wnt and LIF in maintaining pluripotency of mouse ES cells. Biochem Biophys Res Commun 343, 159–166.
Okamoto, K., Okazawa, H., Okuda, A., Sakai, M., Muramatsu, M., Hamada, H., 1990. A novel octamer binding transcription factor is differentially expressed in mouse embryonic cells. Cell 60, 461–472.
Okumura-Nakanishi, S., Saito, M., Niwa, H., Ishikawa, F., 2005. Oct-3/4 and Sox2 regulate Oct-3/4 gene in embryonic stem cells. J Biol Chem 280, 5307–5317.
Palmieri, S.L., Peter, W., Hess, H., Scholer, H.R., 1994. Oct-4 transcription factor is differentially expressed in the mouse embryo during establishment of the first two extraembryonic cell lineages involved in implantation. Dev Biol 166, 259–267.
Papaioannou, V.E., McBurney, M.W., Gardner, R.L., Evans, M.J., 1975. Fate of teratocarcinoma cells injected into early mouse embryos. Nature 258, 70–73.
Park, I.H., Lerou, P.H., Zhao, R., Huo, H., Daley, G.Q., 2008a. Generation of human-induced pluripotent stem cells. Nat Protoc 3, 1180–1186.
Park, I.H., Zhao, R., West, J.A., Yabuuchi, A., Huo, H., Ince, T.A., Lerou, P.H., Lensch, M.W., Daley, G.Q., 2008b. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451, 141–146.
Pasini, D., Bracken, A.P., Jensen, M.R., Lazzerini Denchi, E., Helin, K., 2004. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. Embo J 23, 4061–4071.
Pebay, A., Wong, R.C., Pitson, S.M., Wolvetang, E.J., Peh, G.S., Filipczyk, A., Koh, K.L., Tellis, I., Nguyen, L.T., Pera, M.F., 2005. Essential roles of sphingosine-1-phosphate and platelet-derived growth factor in the maintenance of human embryonic stem cells. Stem Cells 23, 1541–1548.
Pera, E.M., Ikeda, A., Eivers, E., De Robertis, E.M., 2003. Integration of IGF, FGF, and anti-BMP signals via Smad1 phosphorylation in neural induction. Genes Dev 17, 3023–3028.
Pesce, M., Scholer, H.R., 2000. Oct-4: control of totipotency and germline determination. Mol Reprod Dev 55, 452–457.
Pesce, M., Wang, X., Wolgemuth, D.J., Scholer, H., 1998. Differential expression of the Oct-4 transcription factor during mouse germ cell differentiation. Mech Dev 71, 89–98.
Poon, E., Clermont, F., Firpo, M.T., Akhurst, R.J., 2006. TGFbeta inhibition of yolk-sac-like differentiation of human embryonic stem-cell-derived embryoid bodies illustrates differences between early mouse and human development. J Cell Sci 119, 759–768.
Pyle, A.D., Lock, L.F., Donovan, P.J., 2006. Neurotrophins mediate human embryonic stem cell survival. Nat Biotechnol 24, 344–350.
Qi, X., Li, T.G., Hao, J., Hu, J., Wang, J., Simmons, H., Miura, S., Mishina, Y., Zhao, G.Q., 2004. BMP4 supports self-renewal of embryonic stem cells by inhibiting mitogen-activated protein kinase pathways. Proc Natl Acad Sci U S A 101, 6027–6032.
Rehberg, S., Lischka, P., Glaser, G., Stamminger, T., Wegner, M., Rosorius, O., 2002. Sox10 is an active nucleocytoplasmic shuttle protein, and shuttling is crucial for Sox10-mediated transactivation. Mol Cell Biol 22, 5826–5834.
Remenyi, A., Scholer, H.R., Wilmanns, M., 2004. Combinatorial control of gene expression. Nat Struct Mol Biol 11, 812–815.
Richards, M., Tan, S.P., Tan, J.H., Chan, W.K., Bongso, A., 2004. The transcriptome profile of human embryonic stem cells as defined by SAGE. Stem Cells 22, 51–64.
Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., Thiessen, N., Griffith, O.L., He, A., Marra, M., Snyder, M., Jones, S., 2007. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4, 651–657.
Rodda, D.J., Chew, J.L., Lim, L.H., Loh, Y.H., Wang, B., Ng, H.H., Robson, P., 2005. Transcriptional regulation of nanog by OCT4 and SOX2. J Biol Chem 280, 24731–24737.
Sakaki-Yumoto, M., Kobayashi, C., Sato, A., Fujimura, S., Matsumoto, Y., Takasato, M., Kodama, T., Aburatani, H., Asashima, M., Yoshida, N., Nishinakamura, R., 2006. The murine homolog of SALL4, a causative gene in Okihiro syndrome, is essential for embryonic stem cell proliferation, and cooperates with Sall1 in anorectal, heart, brain and kidney development. Development 133, 3005–3013.
Sato, N., Meijer, L., Skaltsounis, L., Greengard, P., Brivanlou, A.H., 2004. Maintenance of pluripotency in human and mouse embryonic stem cells through activation of Wnt signaling by a pharmacological GSK-3-specific inhibitor. Nat Med 10, 55–63.
Scholer, H.R., Dressler, G.R., Balling, R., Rohdewohld, H., Gruss, P., 1990. Oct-4: a germline-specific transcription factor mapping to the mouse t-complex. Embo J 9, 2185–2195.
Scholer, H.R., Hatzopoulos, A.K., Balling, R., Suzuki, N., Gruss, P., 1989. A family of octamer-specific proteins present during mouse embryogenesis: evidence for germline-specific expression of an Oct factor. Embo J 8, 2543–2550.
Sharov, A.A., Piao, Y., Matoba, R., Dudekula, D.B., Qian, Y., VanBuren, V., Falco, G., Martin, P.R., Stagg, C.A., Bassey, U.C., Wang, Y., Carter, M.G., Hamatani, T., Aiba, K., Akutsu, H., Sharova, L., Tanaka, T.S., Kimber, W.L., Yoshikawa, T., Jaradat, S.A., Pantano, S., Nagaraja, R., Boheler, K.R., Taub, D., Hodes, R.J., Longo, D.L., Schlessinger, D., Keller, J., Klotz, E., Kelsoe, G., Umezawa, A., Vescovi, A.L., Rossant, J., Kunath, T., Hogan, B.L., Curci, A., D'Urso, M., Kelso, J., Hide, W., Ko, M.S., 2003. Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol 1, E74.
Shcherbata, H.R., Hatfield, S., Ward, E.J., Reynolds, S., Fischer, K.A., Ruohola-Baker, H., 2006. The MicroRNA pathway plays a regulatory role in stem cell division. Cell Cycle 5, 172–175.
Shen, X., Liu, Y., Hsu, Y.J., Fujiwara, Y., Kim, J., Mao, X., Yuan, G.C., Orkin, S.H., in press. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in the maintenance of embryonic stem cell identity and pluripotency. Molecular Cell 32(4), 491–502.
Shi, Y., Lan, F., Matson, C., Mulligan, P., Whetstine, J.R., Cole, P.A., Casero, R.A., Shi, Y., 2004. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941–953.
Shiota, K., Kogo, Y., Ohgane, J., Imamura, T., Urano, A., Nishino, K., Tanaka, S., Hattori, N., 2002. Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice. Genes Cells 7, 961–969.
Simon, J.A., Tamkun, J.W., 2002. Programming off and on states in chromatin: mechanisms of Polycomb and trithorax group complexes. Curr Opin Genet Dev 12, 210–218.
Singh, A.M., Hamazaki, T., Hankowski, K.E., Terada, N., 2007. A heterogeneous expression pattern for Nanog in embryonic stem cells. Stem Cells 25, 2534–2542.
Singla, D.K., Schneider, D.J., LeWinter, M.M., Sobel, B.E., 2006. wnt3a but not wnt11 supports self-renewal of embryonic stem cells. Biochem Biophys Res Commun 345, 789–795.
Smith, A.G., Heath, J.K., Donaldson, D.D., Wong, G.G., Moreau, J., Stahl, M., Rogers, D., 1988. Inhibition of pluripotential embryonic stem cell differentiation by purified polypeptides. Nature 336, 688–690.
Smith, J.R., Vallier, L., Lupo, G., Alexander, M., Harris, W.A., Pedersen, R.A., 2008. Inhibition of Activin/Nodal signaling promotes specification of human embryonic stem cells into neuroectoderm. Dev Biol 313, 107–117.
Soh, B.S., Song, C.M., Vallier, L., Li, P., Choong, C., Yeo, B.H., Lim, E.H., Pedersen, R.A., Yang, H.H., Rao, M., Lim, B., 2007. Pleiotrophin enhances clonal growth and long-term expansion of human embryonic stem cells. Stem Cells 25, 3029–3037.
Sparmann, A., Van Lohuizen, M., 2006. Polycomb silencers control cell fate, development and cancer. Nat Rev Cancer 6, 846–856.
Stadler, B.M., Ruohola-Baker, H., 2008. Small RNAs: keeping stem cells in line. Cell 132, 563–566.
Stevens, L.C., Litle, C.C., 1954. Spontaneous testicular teratomas in an inbred strain of mice. Proc Natl Acad Sci U S A 40, 1080–1087.
Stewart, C.L., Kaspar, P., Brunet, L.J., Bhatt, H., Gadi, I., Kontgen, F., Abbondanzo, S.J., 1992. Blastocyst implantation depends on maternal expression of leukaemia inhibitory factor. Nature 359, 76–79.
Sumi, T., Tsuneyoshi, N., Nakatsuji, N., Suemori, H., 2008. Defining early lineage specification of human embryonic stem cells by the orchestrated balance of canonical Wnt/{beta}-catenin, Activin/Nodal and BMP signaling. Development 135(17), 2969–2979.
Suzuki, A., Raya, A., Kawakami, Y., Morita, M., Matsui, T., Nakashima, K., Gage, F.H., Rodriguez-Esteban, C., Izpisua Belmonte, J.C., 2006. Nanog binds to Smad1 and blocks bone morphogenetic protein-induced differentiation of embryonic stem cells. Proc Natl Acad Sci U S A 103, 10294–10299.
Takahashi, K., Okita, K., Nakagawa, M., Yamanaka, S., 2007a. Induction of pluripotent stem cells from fibroblast cultures. Nat Protoc 2, 3081–3089.
Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K., Yamanaka, S., 2007b. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861–872.
Takahashi, K., Yamanaka, S., 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676.
Takeda, K., Noguchi, K., Shi, W., Tanaka, T., Matsumoto, M., Yoshida, N., Kishimoto, T., Akira, S., 1997. Targeted disruption of the mouse Stat3 gene leads to early embryonic lethality. Proc Natl Acad Sci U S A 94, 3801–3804.
Tanaka, T.S., Kunath, T., Kimber, W.L., Jaradat, S.A., Stagg, C.A., Usuda, M., Yokota, T., Niwa, H., Rossant, J., Ko, M.S., 2002. Gene expression profiling of embryo-derived stem cells reveals candidate genes associated with pluripotency and lineage specificity. Genome Res 12, 1921–1928.
Thomson, J.A., Itskovitz-Eldor, J., Shapiro, S.S., Waknitz, M.A., Swiergiel, J.J., Marshall, V.S., Jones, J.M., 1998. Embryonic stem cell lines derived from human blastocysts. Science 282, 1145–1147.
Tokuzawa, Y., Kaiho, E., Maruyama, M., Takahashi, K., Mitsui, K., Maeda, M., Niwa, H., Yamanaka, S., 2003. Fbx15 is a novel target of Oct3/4 but is dispensable for embryonic stem cell self-renewal and mouse development. Mol Cell Biol 23, 2699–2708.
Tomioka, M., Nishimoto, M., Miyagi, S., Katayanagi, T., Fukui, N., Niwa, H., Muramatsu, M., Okuda, A., 2002. Identification of Sox-2 regulatory region which is under the control of Oct-3/4-Sox-2 complex. Nucleic Acids Res 30, 3202–3213.
Tsukada, Y., Fang, J., Erdjument-Bromage, H., Warren, M.E., Borchers, C.H., Tempst, P., Zhang, Y., 2006. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439, 811–816.
Uwanogho, D., Rex, M., Cartwright, E.J., Pearl, G., Healy, C., Scotting, P.J., Sharpe, P.T., 1995. Embryonic expression of the chicken Sox2, Sox3 and Sox11 genes suggests an interactive role in neuronal development. Mech Dev 49, 23–36.
Valdimarsdottir, G., Mummery, C., 2005. Functions of the TGFbeta superfamily in human embryonic stem cells. Apmis 113, 773–789.
Vallier, L., Alexander, M., Pedersen, R.A., 2005. Activin/Nodal and FGF pathways cooperate to maintain pluripotency of human embryonic stem cells. J Cell Sci 118, 4495–4509.
van der Stoop, P., Boutsma, E.A., Hulsman, D., Noback, S., Heimerikx, M., Kerkhoven, R.M., Voncken, J.W., Wessels, L.F., Van Lohuizen, M., 2008. Ubiquitin E3 ligase Ring1b/Rnf2 of polycomb repressive complex 1 contributes to stable maintenance of mouse embryonic stem cells. PLoS ONE 3, e2235.
Van Hoof, D., Passier, R., Ward-Van Oostwaard, D., Pinkse, M.W., Heck, A.J., Mummery, C.L., Krijgsveld, J., 2006. A quest for human and mouse embryonic stem cell-specific proteins. Mol Cell Proteomics 5, 1261–1273.
Velculescu, V.E., Zhang, L., Vogelstein, B., Kinzler, K.W., 1995. Serial analysis of gene expression. Science 270, 484–487.
Voncken, J.W., Roelen, B.A., Roefs, M., De Vries, S., Verhoeven, E., Marino, S., Deschamps, J., Van Lohuizen, M., 2003. Rnf2 (Ring1b) deficiency causes gastrulation arrest and cell cycle inhibition. Proc Natl Acad Sci U S A 100, 2468–2473.
Wang, J., Rao, S., Chu, J., Shen, X., Levasseur, D.N., Theunissen, T.W., Orkin, S.H., 2006. A protein interaction network for pluripotency of embryonic stem cells. Nature 444, 364–368.
Wang, L., Schulz, T.C., Sherrer, E.S., Dauphin, D.S., Shin, S., Nelson, A.M., Ware, C.B., Zhan, M., Song, C.Z., Chen, X., Brimble, S.N., McLean, A., Galeano, M.J., Uhl, E.W., D'Amour, K.A., Chesnut, J.D., Rao, M.S., Blau, C.A., Robins, A.J., 2007a. Self-renewal of human embryonic stem cells requires insulin-like growth factor-1 receptor and ERBB2 receptor signaling. Blood 110, 4111–4119.
Wang, Y., Medvid, R., Melton, C., Jaenisch, R., Blelloch, R., 2007b. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat Genet 39, 380–385.
Ware, C.B., Horowitz, M.C., Renshaw, B.R., Hunt, J.S., Liggitt, D., Koblar, S.A., Gliniak, B.C., McKenna, H.J., Papayannopoulou, T., Thoma, B., Et al., 1995. Targeted disruption of the low-affinity leukemia inhibitory factor receptor gene causes placental, skeletal, neural and metabolic defects and results in perinatal death. Development 121, 1283–1299.
Watanabe, S., Umehara, H., Murayama, K., Okabe, M., Kimura, T., Nakano, T., 2006. Activation of Akt signaling is sufficient to maintain pluripotency in mouse and primate embryonic stem cells. Oncogene 25, 2697–2707.
Whetstine, J.R., Nottke, A., Lan, F., Huarte, M., Smolikov, S., Chen, Z., Spooner, E., Li, E., Zhang, G., Colaiacovo, M., Shi, Y., 2006. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125, 467–481.
Williams, R.L., Hilton, D.J., Pease, S., Willson, T.A., Stewart, C.L., Gearing, D.P., Wagner, E.F., Metcalf, D., Nicola, N.A., Gough, N.M., 1988. Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells. Nature 336, 684–687.
Wu, Q., Chen, X., Zhang, J., Loh, Y.H., Low, T.Y., Zhang, W., Zhang, W., Sze, S.K., Lim, B., Ng, H.H., 2006. Sall4 interacts with Nanog and co-occupies Nanog genomic sites in embryonic stem cells. J Biol Chem 281, 24090–24094.
Xiao, L., Yuan, X., Sharkis, S.J., 2006. Activin A maintains self-renewal and regulates fibroblast growth factor, Wnt, and bone morphogenic protein pathways in human embryonic stem cells. Stem Cells 24, 1476–1486.
Xu, R.H., Chen, X., Li, D.S., Li, R., Addicks, G.C., Glennon, C., Zwaka, T.P., Thomson, J.A., 2002. BMP4 initiates human embryonic stem cell differentiation to trophoblast. Nat Biotechnol 20, 1261–1264.
Xu, R.H., Peck, R.M., Li, D.S., Feng, X., Ludwig, T., Thomson, J.A., 2005. Basic FGF and suppression of BMP signaling sustain undifferentiated proliferation of human ES cells. Nat Methods 2, 185–190.
Xu, R.H., Sampsell-Barron, T.L., Gu, F., Root, S., Peck, R.M., Pan, G., Yu, J., Antosiewicz-Bourget, J., Tian, S., Stewart, R., Thomson, J.A., 2008. NANOG is a direct target of TGFbeta/activin-mediated SMAD signaling in human ESCs. Cell Stem Cell 3, 196–206.
Yamanaka, S., 2008. Pluripotency and nuclear reprogramming. Philos Trans R Soc Lond B Biol Sci 363(1500), 2079–2087.
Yamane, K., Toumazou, C., Tsukada, Y., Erdjument-Bromage, H., Tempst, P., Wong, J., Zhang, Y., 2006. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125, 483–495.
Yang, W.J., Yang, D.D., Na, S., Sandusky, G.E., Zhang, Q., Zhao, G., 2005. Dicer is required for embryonic angiogenesis during mouse development. J Biol Chem 280, 9330–9335.
Yeom, Y.I., Ha, H.S., Balling, R., Scholer, H.R., Artzt, K., 1991. Structure, expression and chromosomal location of the Oct-4 gene. Mech Dev 35, 171–179.
Ying, Q.L., Nichols, J., Chambers, I., Smith, A., 2003. BMP induction of Id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3. Cell 115, 281–292.
Yoshida, K., Chambers, I., Nichols, J., Smith, A., Saito, M., Yasukawa, K., Shoyab, M., Taga, T., Kishimoto, T., 1994. Maintenance of the pluripotential phenotype of embryonic stem cells through direct activation of gp130 signalling pathways. Mech Dev 45, 163–171.
Yoshida, K., Taga, T., Saito, M., Suematsu, S., Kumanogoh, A., Tanaka, T., Fujiwara, H., Hirata, M., Yamagami, T., Nakahata, T., Hirabayashi, T., Yoneda, Y., Tanaka, K., Wang, W.Z., Mori, C., Shiota, K., Yoshida, N., Kishimoto, T., 1996. Targeted disruption of gp130, a common signal transducer for the interleukin 6 family of cytokines, leads to myocardial and hematological disorders. Proc Natl Acad Sci U S A 93, 407–411.
Yuan, H., Corbi, N., Basilico, C., Dailey, L., 1995. Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3. Genes Dev 9, 2635–2645.
Zappone, M.V., Galli, R., Catena, R., Meani, N., De Biasi, S., Mattei, E., Tiveron, C., Vescovi, A.L., Lovell-Badge, R., Ottolenghi, S., Nicolis, S.K., 2000. Sox2 regulatory sequences direct expression of a (beta)-geo transgene to telencephalic neural stem cells and precursors of the mouse embryo, revealing regionalization of gene expression in CNS stem cells. Development 127, 2367–2382.
Zhang, B., Pan, X., Anderson, T.A., 2006a. MicroRNA: a new player in stem cells. J Cell Physiol 209, 266–269.
Zhang, J., Tam, W.L., Tong, G.Q., Wu, Q., Chan, H.Y., Soh, B.S., Lou, Y., Yang, J., Ma, Y., Chai, L., Ng, H.H., Lufkin, T., Robson, P., Lim, B., 2006b. Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1. Nat Cell Biol 8, 1114–1123.
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Fujiwara, Y., Orkin, S.H. (2009). Molecular Regulation of the State of Embryonic Stem Cells. In: Majumder, S. (eds) Stem Cells and Cancer. Springer, New York, NY. https://doi.org/10.1007/978-0-387-89611-3_2
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