Control of the Embryonic Stem Cell State

Cell - Tập 144 - Trang 940-954 - 2011
Richard A. Young1,2
1Whitehead Institute for Biomedical Research, Cambridge, MA 02142 USA
2Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA

Tài liệu tham khảo

Alarcon, 2009, Nuclear CDKs drive Smad transcriptional activation and turnover in BMP and TGF-beta pathways, Cell, 139, 757, 10.1016/j.cell.2009.09.035 Ambrosetti, 2000, Modulation of the activity of multiple transcriptional activation domains by the DNA binding domains mediates the synergistic action of Sox2 and Oct-3 on the fibroblast growth factor-4 enhancer, J. Biol. Chem., 275, 23387, 10.1074/jbc.M000932200 Avilion, 2003, Multipotent cell lineages in early mouse development depend on SOX2 function, Genes Dev., 17, 126, 10.1101/gad.224503 Azuara, 2006, Chromatin signatures of pluripotent cell lines, Nat. Cell Biol., 8, 532, 10.1038/ncb1403 Bartel, 2009, MicroRNAs: Target recognition and regulatory functions, Cell, 136, 215, 10.1016/j.cell.2009.01.002 Beattie, 2005, Activin A maintains pluripotency of human embryonic stem cells in the absence of feeder layers, Stem Cells, 23, 489, 10.1634/stemcells.2004-0279 Ben-Porath, 2008, An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors, Nat. Genet., 40, 499, 10.1038/ng.127 Ben-Shushan, 1995, A dynamic balance between ARP-1/COUP-TFII, EAR-3/COUP-TFI, and retinoic acid receptor:retinoid X receptor heterodimers regulates Oct-3/4 expression in embryonal carcinoma cells, Mol. Cell. Biol., 15, 1034, 10.1128/MCB.15.2.1034 Bernstein, 2006, A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell, 125, 315, 10.1016/j.cell.2006.02.041 Beroukhim, 2010, The landscape of somatic copy-number alteration across human cancers, Nature, 463, 899, 10.1038/nature08822 Bilodeau, 2009, SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state, Genes Dev., 23, 2484, 10.1101/gad.1837309 Boland, 2009, Adult mice generated from induced pluripotent stem cells, Nature, 461, 91, 10.1038/nature08310 Bonasio, 2010, Molecular signals of epigenetic states, Science, 330, 612, 10.1126/science.1191078 Boyer, 2005, Core transcriptional regulatory circuitry in human embryonic stem cells, Cell, 122, 947, 10.1016/j.cell.2005.08.020 Boyer, 2006, Polycomb complexes repress developmental regulators in murine embryonic stem cells, Nature, 441, 349, 10.1038/nature04733 Bracken, 2009, Polycomb group proteins: navigators of lineage pathways led astray in cancer, Nat. Rev. Cancer, 9, 773, 10.1038/nrc2736 Bracken, 2006, Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions, Genes Dev., 20, 1123, 10.1101/gad.381706 Britten, 1969, Gene regulation for higher cells: a theory, Science, 165, 349, 10.1126/science.165.3891.349 Brownell, 1996, Tetrahymena histone acetyltransferase A: A homolog to yeast Gcn5p linking histone acetylation to gene activation, Cell, 84, 843, 10.1016/S0092-8674(00)81063-6 Buhler, 2007, Transcription and RNAi in heterochromatic gene silencing, Nat. Struct. Mol. Biol., 14, 1041, 10.1038/nsmb1315 Cammas, 2004, Association of the transcriptional corepressor TIF1beta with heterochromatin protein 1 (HP1): an essential role for progression through differentiation, Genes Dev., 18, 2147, 10.1101/gad.302904 Cartwright, 2005, LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent mechanism, Development, 132, 885, 10.1242/dev.01670 Chambers, 2004, Self-renewal of teratocarcinoma and embryonic stem cells, Oncogene, 23, 7150, 10.1038/sj.onc.1207930 Chambers, 2003, Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells, Cell, 113, 643, 10.1016/S0092-8674(03)00392-1 Chambers, 2007, Nanog safeguards pluripotency and mediates germline development, Nature, 450, 1230, 10.1038/nature06403 Chen, 2008, Transcriptional regulatory networks in embryonic stem cells, Cold Spring Harb. Symp. Quant. Biol., 73, 203, 10.1101/sqb.2008.73.026 Chen, 2008, Integration of external signaling pathways with the core transcriptional network in embryonic stem cells, Cell, 133, 1106, 10.1016/j.cell.2008.04.043 Chew, 2005, Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells, Mol. Cell. Biol., 25, 6031, 10.1128/MCB.25.14.6031-6046.2005 Chia, 2010, A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity, Nature, 468, 316, 10.1038/nature09531 Clapier, 2009, The biology of chromatin remodeling complexes, Annu. Rev. Biochem., 78, 273, 10.1146/annurev.biochem.77.062706.153223 Cole, 2008, Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells, Genes Dev., 22, 746, 10.1101/gad.1642408 Conaway, 2005, The mammalian Mediator complex and its role in transcriptional regulation, Trends Biochem. Sci., 30, 250, 10.1016/j.tibs.2005.03.002 Core, 2008, Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters, Science, 322, 1845, 10.1126/science.1162228 Cote, 1994, Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex, Science, 265, 53, 10.1126/science.8016655 Deato, 2007, Switching of the core transcription machinery during myogenesis, Genes Dev., 21, 2137, 10.1101/gad.1583407 Deato, 2008, MyoD targets TAF3/TRF3 to activate myogenin transcription, Mol. Cell, 32, 96, 10.1016/j.molcel.2008.09.009 Dejosez, 2008, Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells, Cell, 133, 1162, 10.1016/j.cell.2008.05.047 Dejosez, 2010, Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells, Genes Dev., 24, 1479, 10.1101/gad.1935210 Ding, 2009, 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, 10.1016/j.stem.2009.03.009 Ding, 2008, Mediator links epigenetic silencing of neuronal gene expression with x-linked mental retardation, Mol. Cell, 31, 347, 10.1016/j.molcel.2008.05.023 Dodge, 2004, Histone H3-K9 methyltransferase ESET is essential for early development, Mol. Cell. Biol., 24, 2478, 10.1128/MCB.24.6.2478-2486.2004 Endoh, 2008, Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity, Development, 135, 1513, 10.1242/dev.014340 Farh, 2005, The widespread impact of mammalian MicroRNAs on mRNA repression and evolution, Science, 310, 1817, 10.1126/science.1121158 Fazzio, 2010, Condensin complexes regulate mitotic progression and interphase chromatin structure in embryonic stem cells, J. Cell Biol., 188, 491, 10.1083/jcb.200908026 Fazzio, 2008, An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identity, Cell, 134, 162, 10.1016/j.cell.2008.05.031 Feldman, 2006, G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis, Nat. Cell Biol., 8, 188, 10.1038/ncb1353 Firestein, 2008, CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity, Nature, 455, 547, 10.1038/nature07179 Frankel, 2010, Phenotypic robustness conferred by apparently redundant transcriptional enhancers, Nature, 466, 490, 10.1038/nature09158 Fryer, 2004, Mastermind recruits CycC:CDK8 to phosphorylate the Notch ICD and coordinate activation with turnover, Mol. Cell, 16, 509, 10.1016/j.molcel.2004.10.014 Fuda, 2009, Defining mechanisms that regulate RNA polymerase II transcription in vivo, Nature, 461, 186, 10.1038/nature08449 Fuhrmann, 2001, Mouse germline restriction of Oct4 expression by germ cell nuclear factor, Dev. Cell, 1, 377, 10.1016/S1534-5807(01)00038-7 Fujita, 2008, Caspase activity mediates the differentiation of embryonic stem cells, Cell Stem Cell, 2, 595, 10.1016/j.stem.2008.04.001 Galan-Caridad, 2007, Zfx controls the self-renewal of embryonic and hematopoietic stem cells, Cell, 129, 345, 10.1016/j.cell.2007.03.014 Gao, 2009, Ubiquitin ligase Nedd4L targets activated Smad2/3 to limit TGF-beta signaling, Mol. Cell, 36, 457, 10.1016/j.molcel.2009.09.043 Gaspar-Maia, 2009, Chd1 regulates open chromatin and pluripotency of embryonic stem cells, Nature, 460, 863, 10.1038/nature08212 Giraldez, 2006, Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs, Science, 312, 75, 10.1126/science.1122689 Graf, 2009, Forcing cells to change lineages, Nature, 462, 587, 10.1038/nature08533 Grewal, 2007, Transcription and RNA interference in the formation of heterochromatin, Nature, 447, 399, 10.1038/nature05914 Guenther, 2010, Transcription. Repressive transcription, Science, 329, 150, 10.1126/science.1193995 Guenther, 2007, A chromatin landmark and transcription initiation at most promoters in human cells, Cell, 130, 77, 10.1016/j.cell.2007.05.042 Guenther, 2010, Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells, Cell Stem Cell, 7, 249, 10.1016/j.stem.2010.06.015 Gupta, 2010, Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis, Nature, 464, 1071, 10.1038/nature08975 Han, 1988, Nucleosome loss activates yeast downstream promoters in vivo, Cell, 55, 1137, 10.1016/0092-8674(88)90258-9 Hanna, 2010, Pluripotency and cellular reprogramming: Facts, hypotheses, unresolved issues, Cell, 143, 508, 10.1016/j.cell.2010.10.008 Hart, 2004, Identification, cloning and expression analysis of the pluripotency promoting Nanog genes in mouse and human, Dev. Dyn., 230, 187, 10.1002/dvdy.20034 He, 2005, A microRNA polycistron as a potential human oncogene, Nature, 435, 828, 10.1038/nature03552 He, 2008, The antisense transcriptomes of human cells, Science, 322, 1855, 10.1126/science.1163853 Ho, 2010, Chromatin remodelling during development, Nature, 463, 474, 10.1038/nature08911 Hong, 2008, Shadow enhancers as a source of evolutionary novelty, Science, 321, 1314, 10.1126/science.1160631 Hu, 2009, A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal, Genes Dev., 23, 837, 10.1101/gad.1769609 Imbalzano, 1994, Facilitated binding of TATA-binding protein to nucleosomal DNA, Nature, 370, 481, 10.1038/370481a0 Ivanova, 2006, Dissecting self-renewal in stem cells with RNA interference, Nature, 442, 533, 10.1038/nature04915 Jackson, 2004, Severe global DNA hypomethylation blocks differentiation and induces histone hyperacetylation in embryonic stem cells, Mol. Cell. Biol., 24, 8862, 10.1128/MCB.24.20.8862-8871.2004 Jacob, 1961, Genetic regulatory mechanisms in the synthesis of proteins, J. Mol. Biol., 3, 318, 10.1016/S0022-2836(61)80072-7 Jaenisch, 2008, Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming, Cell, 132, 567, 10.1016/j.cell.2008.01.015 James, 2005, TGFbeta/activin/nodal signaling is necessary for the maintenance of pluripotency in human embryonic stem cells, Development, 132, 1273, 10.1242/dev.01706 Jiang, 2008, A core Klf circuitry regulates self-renewal of embryonic stem cells, Nat. Cell Biol., 10, 353, 10.1038/ncb1698 Kagey, 2010, Mediator and cohesin connect gene expression and chromatin architecture, Nature, 467, 430, 10.1038/nature09380 Kanellopoulou, 2005, Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing, Genes Dev., 19, 489, 10.1101/gad.1248505 Kang, 2009, iPS cells can support full-term development of tetraploid blastocyst-complemented embryos, Cell Stem Cell, 5, 135, 10.1016/j.stem.2009.07.001 Kanhere, 2010, Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2, Mol. Cell, 38, 675, 10.1016/j.molcel.2010.03.019 Kayne, 1988, Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast, Cell, 55, 27, 10.1016/0092-8674(88)90006-2 Kim, 2008, An extended transcriptional network for pluripotency of embryonic stem cells, Cell, 132, 1049, 10.1016/j.cell.2008.02.039 Kim, 2010, A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs, Cell, 143, 313, 10.1016/j.cell.2010.09.010 Kim, 2010, Epigenetic memory in induced pluripotent stem cells, Nature, 467, 285, 10.1038/nature09342 Klochendler-Yeivin, 2000, The murine SNF5/INI1 chromatin remodeling factor is essential for embryonic development and tumor suppression, EMBO Rep., 1, 500, 10.1093/embo-reports/kvd129 Knezetic, 1986, The presence of nucleosomes on a DNA template prevents initiation by RNA polymerase II in vitro, Cell, 45, 95, 10.1016/0092-8674(86)90541-6 Knuesel, 2009, The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function, Genes Dev., 23, 439, 10.1101/gad.1767009 Kornberg, 1974, Chromatin structure; oligomers of the histones, Science, 184, 865, 10.1126/science.184.4139.865 Krantz, 2004, Cornelia de Lange syndrome is caused by mutations in NIPBL, the human homolog of Drosophila melanogaster Nipped-B, Nat. Genet., 36, 631, 10.1038/ng1364 Krivtsov, 2007, MLL translocations, histone modifications and leukaemia stem-cell development, Nat. Rev. Cancer, 7, 823, 10.1038/nrc2253 Krogan, 2003, The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation, Mol. Cell, 11, 721, 10.1016/S1097-2765(03)00091-1 Kwon, 1994, Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex, Nature, 370, 477, 10.1038/370477a0 Landeira, 2010, 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, 10.1038/ncb2065 Lee, 2009, Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome, Genes Dev., 23, 1831, 10.1101/gad.1811209 Lee, 2006, Control of developmental regulators by Polycomb in human embryonic stem cells, Cell, 125, 301, 10.1016/j.cell.2006.02.043 Leeb, 2010, Polycomb complexes act redundantly to repress genomic repeats and genes, Genes Dev., 24, 265, 10.1101/gad.544410 Levine, 2003, Transcription regulation and animal diversity, Nature, 424, 147, 10.1038/nature01763 Li, 2007, The role of chromatin during transcription, Cell, 128, 707, 10.1016/j.cell.2007.01.015 Li, 2010, Jarid2 and PRC2, partners in regulating gene expression, Genes Dev., 24, 368, 10.1101/gad.1886410 Liang, 2008, Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells, Nat. Cell Biol., 10, 731, 10.1038/ncb1736 Lister, 2011, Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells, Nature, 10.1038/nature09798 Lluis, 2008, Periodic activation of Wnt/beta-catenin signaling enhances somatic cell reprogramming mediated by cell fusion, Cell Stem Cell, 3, 493, 10.1016/j.stem.2008.08.017 Loh, 2006, The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells, Nat. Genet., 38, 431, 10.1038/ng1760 Lorch, 1987, Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones, Cell, 49, 203, 10.1016/0092-8674(87)90561-7 Macarthur, 2009, Systems biology of stem cell fate and cellular reprogramming, Nat. Rev. Mol. Cell Biol., 10, 672, 10.1038/nrm2766 Malik, 2005, Dynamic regulation of pol II transcription by the mammalian Mediator complex, Trends Biochem. Sci., 30, 256, 10.1016/j.tibs.2005.03.009 Maniatis, 1998, Structure and function of the interferon-beta enhanceosome, Cold Spring Harb. Symp. Quant. Biol., 63, 609, 10.1101/sqb.1998.63.609 Margueron, 2009, Role of the polycomb protein EED in the propagation of repressive histone marks, Nature, 461, 762, 10.1038/nature08398 Marson, 2008, Wnt signaling promotes reprogramming of somatic cells to pluripotency, Cell Stem Cell, 3, 132, 10.1016/j.stem.2008.06.019 Marson, 2008, Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells, Cell, 134, 521, 10.1016/j.cell.2008.07.020 Masui, 2007, Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells, Nat. Cell Biol., 9, 625, 10.1038/ncb1589 Matoba, 2006, Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression profiling, PLoS ONE, 1, e26, 10.1371/journal.pone.0000026 Meissner, 2010, Epigenetic modifications in pluripotent and differentiated cells, Nat. Biotechnol., 28, 1079, 10.1038/nbt.1684 Melton, 2010, Opposing microRNA families regulate self-renewal in mouse embryonic stem cells, Nature, 463, 621, 10.1038/nature08725 Mitsui, 2003, The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells, Cell, 113, 631, 10.1016/S0092-8674(03)00393-3 Muncke, 2003, Missense mutations and gene interruption in PROSIT240, a novel TRAP240-like gene, in patients with congenital heart defect (transposition of the great arteries), Circulation, 108, 2843, 10.1161/01.CIR.0000103684.77636.CD Murchison, 2005, Characterization of Dicer-deficient murine embryonic stem cells, Proc. Natl. Acad. Sci. USA, 102, 12135, 10.1073/pnas.0505479102 Nasmyth, 2009, Cohesin: its roles and mechanisms, Annu. Rev. Genet., 43, 525, 10.1146/annurev-genet-102108-134233 Niakan, 2006, Novel role for the orphan nuclear receptor Dax1 in embryogenesis, different from steroidogenesis, Mol. Genet. Metab., 88, 261, 10.1016/j.ymgme.2005.12.010 Nichols, 1998, Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4, Cell, 95, 379, 10.1016/S0092-8674(00)81769-9 Niwa, 2007, How is pluripotency determined and maintained?, Development, 134, 635, 10.1242/dev.02787 Niwa, 1998, Self-renewal of pluripotent embryonic stem cells is mediated via activation of STAT3, Genes Dev., 12, 2048, 10.1101/gad.12.13.2048 Niwa, 2000, Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells, Nat. Genet., 24, 372, 10.1038/74199 Niwa, 2009, A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells, Nature, 460, 118, 10.1038/nature08113 O'Donnell, 2005, c-Myc-regulated microRNAs modulate E2F1 expression, Nature, 435, 839, 10.1038/nature03677 Okita, 2006, Intracellular signaling pathways regulating pluripotency of embryonic stem cells, Curr. Stem Cell Res. Ther., 1, 103, 10.2174/157488806775269061 Olins, 1974, Spheroid chromatin units (v bodies), Science, 183, 330, 10.1126/science.183.4122.330 Orkin, 2008, The transcriptional network controlling pluripotency in ES cells, Cold Spring Harb. Symp. Quant. Biol., 73, 195, 10.1101/sqb.2008.72.001 Pan, 2007, Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells, Cell Stem Cell, 1, 299, 10.1016/j.stem.2007.08.003 Pandey, 2008, Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation, Mol. Cell, 32, 232, 10.1016/j.molcel.2008.08.022 Pardo, 2010, An expanded Oct4 interaction network: Implications for stem cell biology, development, and disease, Cell Stem Cell, 6, 382, 10.1016/j.stem.2010.03.004 Pasini, 2004, Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity, EMBO J., 23, 4061, 10.1038/sj.emboj.7600402 Pasini, 2008, Regulation of stem cell differentiation by histone methyltransferases and demethylases, Cold Spring Harb. Symp. Quant. Biol., 73, 253, 10.1101/sqb.2008.73.009 Pasini, 2010, JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells, Nature, 464, 306, 10.1038/nature08788 Peng, 2009, Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells, Cell, 139, 1290, 10.1016/j.cell.2009.12.002 Pera, 2010, Extrinsic regulation of pluripotent stem cells, Nature, 465, 713, 10.1038/nature09228 Peterlin, 2006, Controlling the elongation phase of transcription with P-TEFb, Mol. Cell, 23, 297, 10.1016/j.molcel.2006.06.014 Philibert, 2007, Role of MED12 in transcription and human behavior, Pharmacogenomics, 8, 909, 10.2217/14622416.8.8.909 Polo, 2010, Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells, Nat. Biotechnol., 28, 848, 10.1038/nbt.1667 Rahl, 2010, c-Myc regulates transcriptional pause release, Cell, 141, 432, 10.1016/j.cell.2010.03.030 Rinn, 2007, Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs, Cell, 129, 1311, 10.1016/j.cell.2007.05.022 Risheg, 2007, A recurrent mutation in MED12 leading to R961W causes Opitz-Kaveggia syndrome, Nat. Genet., 39, 451, 10.1038/ng1992 Roeder, 1998, Role of general and gene-specific cofactors in the regulation of eukaryotic transcription, Cold Spring Harb. Symp. Quant. Biol., 63, 201, 10.1101/sqb.1998.63.201 Roeder, 2005, Transcriptional regulation and the role of diverse coactivators in animal cells, FEBS Lett., 579, 909, 10.1016/j.febslet.2004.12.007 Rossant, 2008, Stem cells and early lineage development, Cell, 132, 527, 10.1016/j.cell.2008.01.039 Sato, 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, 10.1038/nm979 Schnetz, 2010, CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression, PLoS Genet., 6, e1001023, 10.1371/journal.pgen.1001023 Schuettengruber, 2007, Genome regulation by polycomb and trithorax proteins, Cell, 128, 735, 10.1016/j.cell.2007.02.009 Scholer, 1990, New type of POU domain in germ line-specific protein Oct-4, Nature, 344, 435, 10.1038/344435a0 Schultz, 2002, SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins, Genes Dev., 16, 919, 10.1101/gad.973302 Schwartz, 2007, The original Lujan syndrome family has a novel missense mutation (p.N1007S) in the MED12 gene, J. Med. Genet., 44, 472, 10.1136/jmg.2006.048637 Seila, 2008, Divergent transcription from active promoters, Science, 322, 1849, 10.1126/science.1162253 Shen, 2009, Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells, Cell, 139, 1303, 10.1016/j.cell.2009.12.003 Silva, 2008, Capturing pluripotency, Cell, 132, 532, 10.1016/j.cell.2008.02.006 Silva, 2009, Nanog is the gateway to the pluripotent ground state, Cell, 138, 722, 10.1016/j.cell.2009.07.039 Smith, 2001, Embryo-derived stem cells: of mice and men, Annu. Rev. Cell Dev. Biol., 17, 435, 10.1146/annurev.cellbio.17.1.435 Smith, 1998, The role of leukemia inhibitory factor and interleukin-6 in human reproduction, Hum. Reprod., 13, 237, 10.1093/humrep/13.suppl_3.237 Smith, 1983, Medium conditioned by feeder cells inhibits the differentiation of embryonal carcinoma cultures, Exp. Cell Res., 145, 458, 10.1016/0014-4827(83)90025-3 Stadtfeld, 2010, Induced pluripotency: history, mechanisms, and applications, Genes Dev., 24, 2239, 10.1101/gad.1963910 Stadtfeld, 2010, Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells, Nature, 465, 175, 10.1038/nature09017 Stock, 2007, Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells, Nat. Cell Biol., 9, 1428, 10.1038/ncb1663 Strachan, 2005, Cornelia de Lange Syndrome and the link between chromosomal function, DNA repair and developmental gene regulation, Curr. Opin. Genet. Dev., 15, 258, 10.1016/j.gde.2005.04.005 Sun, 2009, Dax1 binds to Oct3/4 and inhibits its transcriptional activity in embryonic stem cells, Mol. Cell. Biol., 29, 4574, 10.1128/MCB.01863-08 Surface, 2010, Polycomb group proteins set the stage for early lineage commitment, Cell Stem Cell, 7, 288, 10.1016/j.stem.2010.08.004 Taatjes, 2010, The human Mediator complex: a versatile, genome-wide regulator of transcription, Trends Biochem. Sci., 35, 315, 10.1016/j.tibs.2010.02.004 Tam, 2008, T-cell factor 3 regulates embryonic stem cell pluripotency and self-renewal by the transcriptional control of multiple lineage pathways, Stem Cells, 26, 2019, 10.1634/stemcells.2007-1115 Tay, 2008, MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation, Nature, 455, 1124, 10.1038/nature07299 Tonkin, 2004, NIPBL, encoding a homolog of fungal Scc2-type sister chromatid cohesion proteins and fly Nipped-B, is mutated in Cornelia de Lange syndrome, Nat. Genet., 36, 636, 10.1038/ng1363 Tsai, 2010, Long noncoding RNA as modular scaffold of histone modification complexes, Science, 329, 689, 10.1126/science.1192002 Vallier, 2005, Activin/Nodal and FGF pathways cooperate to maintain pluripotency of human embryonic stem cells, J. Cell Sci., 118, 4495, 10.1242/jcs.02553 van den Berg, 2010, An Oct4-centered protein interaction network in embryonic stem cells, Cell Stem Cell, 6, 369, 10.1016/j.stem.2010.02.014 van der Stoop, 2008, Ubiquitin E3 ligase Ring1b/Rnf2 of polycomb repressive complex 1 contributes to stable maintenance of mouse embryonic stem cells, PLoS ONE, 3, e2235, 10.1371/journal.pone.0002235 Vaquerizas, 2009, A census of human transcription factors: function, expression and evolution, Nat. Rev. Genet., 10, 252, 10.1038/nrg2538 Vierbuchen, 2010, Direct conversion of fibroblasts to functional neurons by defined factors, Nature, 463, 1035, 10.1038/nature08797 Viswanathan, 2008, Selective blockade of microRNA processing by Lin28, Science, 320, 97, 10.1126/science.1154040 Wang, 2006, A protein interaction network for pluripotency of embryonic stem cells, Nature, 444, 364, 10.1038/nature05284 Wang, 2007, DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal, Nat. Genet., 39, 380, 10.1038/ng1969 Wang, 2008, Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation, Nat. Genet., 40, 1478, 10.1038/ng.250 Williams, 1988, Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells, Nature, 336, 684, 10.1038/336684a0 Wilusz, 2009, Long noncoding RNAs: functional surprises from the RNA world, Genes Dev., 23, 1494, 10.1101/gad.1800909 Wood, 2010, Condensin and cohesin complexity: the expanding repertoire of functions, Nat. Rev. Genet., 11, 391, 10.1038/nrg2794 Wu, 2006, Sall4 interacts with Nanog and co-occupies Nanog genomic sites in embryonic stem cells, J. Biol. Chem., 281, 24090, 10.1074/jbc.C600122200 Yamanaka, 2010, Nuclear reprogramming to a pluripotent state by three approaches, Nature, 465, 704, 10.1038/nature09229 Yap, 2010, Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a, Mol. Cell, 38, 662, 10.1016/j.molcel.2010.03.021 Yeap, 2009, ERG-associated protein with SET domain (ESET)-Oct4 interaction regulates pluripotency and represses the trophectoderm lineage, Epigenetics Chromatin, 2, 12, 10.1186/1756-8935-2-12 Ying, 2003, BMP induction of Id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3, Cell, 115, 281, 10.1016/S0092-8674(03)00847-X Yuan, 2009, Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells, Genes Dev., 23, 2507, 10.1101/gad.1831909 Zaratiegui, 2007, Noncoding RNAs and gene silencing, Cell, 128, 763, 10.1016/j.cell.2007.02.016 Zhang, 2006, Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1, Nat. Cell Biol., 8, 1114, 10.1038/ncb1481 Zhang, 2008, Esrrb activates Oct4 transcription and sustains self-renewal and pluripotency in embryonic stem cells, J. Biol. Chem., 283, 35825, 10.1074/jbc.M803481200 Zhao, 2008, Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome, Science, 322, 750, 10.1126/science.1163045 Zhao, 2010, Genome-wide identification of Polycomb-associated RNAs by RIP-seq, Mol. Cell, 40, 939, 10.1016/j.molcel.2010.12.011 Zhao, 2009, iPS cells produce viable mice through tetraploid complementation, Nature, 461, 86, 10.1038/nature08267 Zhong, 2009, Critical roles of coactivator p300 in mouse embryonic stem cell differentiation and Nanog expression, J. Biol. Chem., 284, 9168, 10.1074/jbc.M805562200 Zhou, 2008, In vivo reprogramming of adult pancreatic exocrine cells to beta-cells, Nature, 455, 627, 10.1038/nature07314 Zhou, 2008, Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation, Mol. Cell, 29, 69, 10.1016/j.molcel.2007.11.002