Combining competition assays with genetic complementation strategies to dissect mouse embryonic stem cell self-renewal and pluripotency (original) (raw)

• Zhang, X. et al. FOXO1 is an essential regulator of pluripotency in human embryonic stem cells. Nat. Cell. Biol. 13, 1092–1099 (2011).
  Article CAS Google Scholar
• Ivanova, N. et al. Dissecting self-renewal in stem cells with RNA interference. Nature 442, 533–538 (2006).
  Article CAS Google Scholar
• Jiang, H. et al. Role for Dpy-30 in ES cell-fate specification by regulation of H3K4 methylation within bivalent domains. Cell 144, 513–525 (2011).
  Article CAS Google Scholar
• Ang, Y.S. et al. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145, 183–197 (2011).
  Article CAS Google Scholar
• Shen, X. et al. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol. Cell 32, 491–502 (2008).
  Article CAS Google Scholar
• Schaniel, C. et al. Smarcc1/Baf155 couples self-renewal gene repression with changes in chromatin structure in mouse embryonic stem cells. Stem Cells 27, 2979–2991 (2009).
  CAS PubMed PubMed Central 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. Cell 134, 162–174 (2008).
  Article CAS Google Scholar
• Singhal, N. et al. Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell 141, 943–955 (2010).
  Article CAS Google Scholar
• Sato, N., Meijer, L., Skaltsounis, L., Greengard, P. & Brivanlou, A.H. 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 (2004).
  Article CAS Google Scholar
• Smith, A.G. et al. Inhibition of pluripotential embryonic stem cell differentiation by purified polypeptides. Nature 336, 688–690 (1988).
  Article CAS Google Scholar
• Williams, R.L. et al. Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells. Nature 336, 684–687 (1988).
  Article CAS 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. Cell 115, 281–292 (2003).
  Article 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 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 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).
  Article CAS Google Scholar
• Kim, J., Chu, J., Shen, X., Wang, J. & Orkin, S.H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049–1061 (2008).
  Article CAS Google Scholar
• Wang, J. et al. A protein interaction network for pluripotency of embryonic stem cells. Nature 444, 364–368 (2006).
  Article 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 Google Scholar
• Pardo, M. et al. An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell 6, 382–395 (2010).
  Article CAS Google Scholar
• van den Berg, D.L. et al. An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 6, 369–381 (2010).
  Article 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 Google Scholar
• Ho, L. et al. An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc. Natl. Acad. Sci. USA 106, 5181–5186 (2009).
  Article CAS 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 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 Google Scholar
• Dejosez, M. et al. Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells. Cell 133, 1162–1174 (2008).
  Article CAS Google Scholar
• Chia, N.Y. et al. A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature 468, 316–320 (2010).
  Article CAS Google Scholar
• Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998).
  Article CAS Google Scholar
• Meister, G. & Tuschl, T. Mechanisms of gene silencing by double-stranded RNA. Nature 431, 343–349 (2004).
  Article CAS Google Scholar
• Brummelkamp, T.R., Bernards, R. & Agami, R. A system for stable expression of short interfering RNAs in mammalian cells. Science 296, 550–553 (2002).
  Article CAS Google Scholar
• Sharp, P.A. RNAi and double-strand RNA. Genes Dev. 13, 139–141 (1999).
  Article CAS Google Scholar
• Schaniel, C. et al. Delivery of short hairpin RNAs—triggers of gene silencing—into mouse embryonic stem cells. Nat. Methods 3, 397–400 (2006).
  Article CAS Google Scholar
• Hannon, G.J. & Rossi, J.J. Unlocking the potential of the human genome with RNA interference. Nature 431, 371–378 (2004).
  Article CAS Google Scholar
• McCaffrey, A.P. et al. RNA interference in adult mice. Nature 418, 38–39 (2002).
  Article CAS Google Scholar
• McManus, M.T., Petersen, C.P., Haines, B.B., Chen, J. & Sharp, P.A. Gene silencing using micro-RNA designed hairpins. RNA 8, 842–850 (2002).
  Article CAS Google Scholar
• Paddison, P.J., Caudy, A.A., Bernstein, E., Hannon, G.J. & Conklin, D.S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16, 948–958 (2002).
  Article CAS Google Scholar
• Paul, C.P., Good, P.D., Winer, I. & Engelke, D.R. Effective expression of small interfering RNA in human cells. Nat. Biotechnol. 20, 505–508 (2002).
  Article CAS Google Scholar
• Sui, G. et al. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA 99, 5515–5520 (2002).
  Article CAS Google Scholar
• Xia, H., Mao, Q., Paulson, H.L. & Davidson, B.L. siRNA-mediated gene silencing in vitro and in vivo. Nat. Biotechnol. 20, 1006–1010 (2002).
  Article CAS Google Scholar
• Yu, J.Y., DeRuiter, S.L. & Turner, D.L. RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 99, 6047–6052 (2002).
  Article CAS Google Scholar
• Schaniel, C., Lee, D.F. & Lemischka, I.R. Exploration of self-renewal and pluripotency in ES cells using RNAi. Methods Enzymol. 477, 351–365 (2010).
  Article CAS Google Scholar
• Lu, R. et al. Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature 462, 358–362 (2009).
  Article CAS Google Scholar
• Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283–1298 (2006).
  Article CAS Google Scholar
• Boheler, K.R. Stem cell pluripotency: a cellular trait that depends on transcription factors, chromatin state and a checkpoint deficient cell cycle. J. Cell Physiol. 221, 10–17 (2009).
  Article CAS Google Scholar
• Savatier, P., Huang, S., Szekely, L., Wiman, K.G. & Samarut, J. Contrasting patterns of retinoblastoma protein expression in mouse embryonic stem cells and embryonic fibroblasts. Oncogene 9, 809–818 (1994).
  CAS PubMed Google Scholar
• Ting, D.T., Kyba, M. & Daley, G.Q. Inducible transgene expression in mouse stem cells. Methods Mol. Med. 105, 23–46 (2005).
  CAS PubMed Google Scholar
• Macarthur, B.D., Ma′ayan, A. & Lemischka, I.R. Systems biology of stem cell fate and cellular reprogramming. Nat. Rev. Mol. Cell Biol. 10, 672–681 (2009).
  Article CAS Google Scholar
• Lewis, D.L., Hagstrom, J.E., Loomis, A.G., Wolff, J.A. & Herweijer, H. Efficient delivery of siRNA for inhibition of gene expression in postnatal mice. Nat. Genet. 32, 107–108 (2002).
  Article CAS Google Scholar
• Tam, P.P. & Rossant, J. Mouse embryonic chimeras: tools for studying mammalian development. Development 130, 6155–6163 (2003).
  Article CAS Google Scholar
• Conner, D.A. Mouse embryo fibroblast (MEF) feeder cell preparation. Curr. Protoc. Mol. Biol. Chapter 23, Unit 23 22 (2001).
• Lachmann, A. et al. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 26, 2438–2444 (2010).
  Article CAS Google Scholar
• Schmittgen, T.D. & Livak, K.J. Analyzing real-time PCR data by the comparative C(T) method. Nat. Protoc. 3, 1101–1108 (2008).
  Article CAS Google Scholar
• Kutner, R.H., Zhang, X.Y. & Reiser, J. Production, concentration and titration of pseudotyped HIV-1-based lentiviral vectors. Nat. Protoc. 4, 495–505 (2009).
  Article CAS Google Scholar