Epigenetic modifications in pluripotent and differentiated cells (original) (raw)
Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev.16, 6–21 (2002). CASPubMed Google Scholar
Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet.33 Suppl, 245–254 (2003). CASPubMed Google Scholar
Yamanaka, S. Strategies and new developments in the generation of patient-specific pluripotent stem cells. Cell Stem Cell1, 39–49 (2007). CASPubMed Google Scholar
Reik, W., Dean, W. & Walter, J. Epigenetic reprogramming in mammalian development. Science293, 1089–1093 (2001). CASPubMed Google Scholar
Rideout, W.M. III, Eggan, K. & Jaenisch, R. Nuclear cloning and epigenetic reprogramming of the genome. Science293, 1093–1098 (2001). CASPubMed Google Scholar
Hammoud, S.S. et al. Distinctive chromatin in human sperm packages genes for embryo development. Nature460, 473–478 (2009). CASPubMedPubMed Central Google Scholar
Oswald, J. et al. Active demethylation of the paternal genome in the mouse zygote. Curr. Biol.10, 475–478 (2000). CASPubMed Google Scholar
Santos, F., Hendrich, B., Reik, W. & Dean, W. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev. Biol.241, 172–182 (2002). CASPubMed Google Scholar
Mayer, W., Niveleau, A., Walter, J., Fundele, R. & Haaf, T. Demethylation of the zygotic paternal genome. Nature403, 501–502 (2000). CASPubMed Google Scholar
Kafri, T. et al. Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. Genes Dev.6, 705–714 (1992). CASPubMed Google Scholar
Lane, N. et al. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis35, 88–93 (2003). CASPubMed Google Scholar
Rossant, J. Stem cells and early lineage development. Cell132, 527–531 (2008). CASPubMed Google Scholar
Niakan, K.K. et al. Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes Dev.24, 312–326 (2010). CASPubMedPubMed Central Google Scholar
Tanaka, S., Kunath, T., Hadjantonakis, A.K., Nagy, A. & Rossant, J. Promotion of trophoblast stem cell proliferation by FGF4. Science282, 2072–2075 (1998). CASPubMed Google Scholar
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
Chen, A.E. et al. Optimal timing of inner cell mass isolation increases the efficiency of human embryonic stem cell derivation and allows generation of sibling cell lines. Cell Stem Cell4, 103–106 (2009). CASPubMedPubMed Central Google Scholar
Cowan, C.A. et al. Derivation of embryonic stem-cell lines from human blastocysts. N. Engl. J. Med.350, 1353–1356 (2004). CASPubMed Google Scholar
Thomson, J.A. et al. Embryonic stem cell lines derived from human blastocysts. Science282, 1145–1147 (1998). CASPubMed Google Scholar
Jaenisch, R. & Young, R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell132, 567–582 (2008). CASPubMedPubMed Central Google Scholar
Jackson-Grusby, L. et al. Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nat. Genet.27, 31–39 (2001). CASPubMed Google Scholar
Okano, M., Xie, S. & Li, E. Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells. Nucleic Acids Res.26, 2536–2540 (1998). CASPubMedPubMed Central Google Scholar
Goll, M.G. et al. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science311, 395–398 (2006). CASPubMed Google Scholar
Li, E., Bestor, T.H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell69, 915–926 (1992). CASPubMed Google Scholar
Okano, M., Bell, D.W., Haber, D.A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell99, 247–257 (1999). CASPubMed Google Scholar
Dodge, J.E. et al. Inactivation of Dnmt3b in mouse embryonic fibroblasts results in DNA hypomethylation, chromosomal instability, and spontaneous immortalization. J. Biol. Chem.280, 17986–17991 (2005). CASPubMed Google Scholar
Kaneda, M. et al. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature429, 900–903 (2004). CASPubMed Google Scholar
Bourc'his, D., Xu, G.L., Lin, C.S., Bollman, B. & Bestor, T.H. Dnmt3L and the establishment of maternal genomic imprints. Science294, 2536–2539 (2001). CASPubMed Google Scholar
Bourc'his, D. & Bestor, T.H. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature431, 96–99 (2004). CASPubMed Google Scholar
Jia, D., Jurkowska, R.Z., Zhang, X., Jeltsch, A. & Cheng, X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature449, 248–251 (2007). CASPubMedPubMed Central Google Scholar
Ooi, S.K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature448, 714–717 (2007). CASPubMedPubMed Central Google Scholar
Hayashi, K. & Surani, M.A. Resetting the epigenome beyond pluripotency in the germline. Cell Stem Cell4, 493–498 (2009). CASPubMed Google Scholar
Popp, C. et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature463, 1101–1105 (2010). CASPubMedPubMed Central Google Scholar
Strahl, B.D. & Allis, C.D. The language of covalent histone modifications. Nature403, 41–45 (2000). CASPubMed Google Scholar
Shi, Y. Histone lysine demethylases: emerging roles in development, physiology and disease. Nat. Rev. Genet.8, 829–833 (2007). CASPubMed Google Scholar
Francis, N.J. & Kingston, R.E. Mechanisms of transcriptional memory. Nat. Rev. Mol. Cell Biol.2, 409–421 (2001). CASPubMed Google Scholar
Campos, E.I. & Reinberg, D. Histones: annotating chromatin. Annu. Rev. Genet.43, 559–599 (2009). CASPubMed Google Scholar
Bernstein, B.E., Meissner, A. & Lander, E.S. The mammalian epigenome. Cell128, 669–681 (2007). CASPubMed Google Scholar
Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science298, 1039–1043 (2002). CASPubMed Google Scholar
Zhang, Y., Cao, R., Wang, L. & Jones, R.S. Mechanism of Polycomb group gene silencing. Cold Spring Harb. Symp. Quant. Biol.69, 309–317 (2004). CASPubMed Google Scholar
Faust, C., Lawson, K.A., Schork, N.J., Thiel, B. & Magnuson, T. The Polycomb-group gene eed is required for normal morphogenetic movements during gastrulation in the mouse embryo. Development125, 4495–4506 (1998). CASPubMed Google Scholar
O'Carroll, D. et al. The polycomb-group gene Ezh2 is required for early mouse development. Mol. Cell. Biol.21, 4330–4336 (2001). CASPubMedPubMed Central Google Scholar
Pasini, D., Bracken, A.P., Jensen, M.R., Lazzerini Denchi, E. & Helin, K. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J.23, 4061–4071 (2004). CASPubMedPubMed Central 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. Cell32, CASPubMedPubMed Central Google Scholar
Ezhkova, E. et al. Ezh2 orchestrates gene expression for the stepwise differentiation of tissue-specific stem cells. Cell136, 1122–1135 (2009). CASPubMedPubMed Central Google Scholar
Shumacher, A., Faust, C. & Magnuson, T. Positional cloning of a global regulator of anterior-posterior patterning in mice. Nature383, 250–253 (1996). CASPubMed Google Scholar
Hanson, R.D. et al. Mammalian Trithorax and polycomb-group homologues are antagonistic regulators of homeotic development. Proc. Natl. Acad. Sci. USA96, 14372–14377 (1999). CASPubMedPubMed Central Google Scholar
van der Lugt, N.M. et al. Posterior transformation, neurological abnormalities, and severe hematopoietic defects in mice with a targeted deletion of the bmi-1 proto-oncogene. Genes Dev.8, 757–769 (1994). CASPubMed Google Scholar
Dodge, J.E., Kang, Y.K., Beppu, H., Lei, H. & Li, E. Histone H3–K9 methyltransferase ESET is essential for early development. Mol. Cell. Biol.24, 2478–2486 (2004). CASPubMedPubMed Central Google Scholar
Tachibana, M. et al. Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3–K9. Genes Dev.19, 815–826 (2005). CASPubMedPubMed Central Google Scholar
Li, E. Chromatin modification and epigenetic reprogramming in mammalian development. Nat. Rev. Genet.3, 662–673 (2002). CASPubMed Google Scholar
Surani, M.A., Hayashi, K. & Hajkova, P. Genetic and epigenetic regulators of pluripotency. Cell128, 747–762 (2007). CASPubMed Google Scholar
Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet.4, e1000242 (2008). PubMedPubMed Central Google Scholar
Zhao, X.D. et al. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell1, 286–298 (2007). CASPubMed Google Scholar
Pan, G. et al. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell1, 299–312 (2007). CASPubMed Google Scholar
Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature448, 553–560 (2007). CASPubMedPubMed Central Google Scholar
Bernstein, B.E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell125, 315–326 (2006). CASPubMed Google Scholar
Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature462, 315–322 (2009). CASPubMedPubMed Central Google Scholar
Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature454, 766–770 (2008). CASPubMedPubMed Central Google Scholar
Mohn, F. et al. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell30, 755–766 (2008). CASPubMed Google Scholar
Meissner, A. et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res.33, 5868–5877 (2005). CASPubMedPubMed Central Google Scholar
Jackson, M. et al. Severe global DNA hypomethylation blocks differentiation and induces histone hyperacetylation in embryonic stem cells. Mol. Cell. Biol.24, 8862–8871 (2004). CASPubMedPubMed Central Google Scholar
Tsumura, A. et al. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells11, 805–814 (2006). CASPubMed Google Scholar
Chamberlain, S.J., Yee, D. & Magnuson, T. Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency. Stem Cells26, 1496–1505 (2008). CASPubMedPubMed Central Google Scholar
Holm, T.M. et al. Global loss of imprinting leads to widespread tumorigenesis in adult mice. Cancer Cell8, 275–285 (2005). CASPubMed Google Scholar
Fouse, S. et al. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell2, 160–169 (2008). CASPubMedPubMed Central Google Scholar
Ng, R.K. et al. Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5. Nat. Cell Biol.10, 1280–1290 (2008). CASPubMedPubMed Central Google Scholar
Boyer, L.A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature441, 349–353 (2006). CASPubMed Google Scholar
Bracken, A.P., Dietrich, N., Pasini, D., Hansen, K.H. & Helin, K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev.20, 1123–1136 (2006). CASPubMedPubMed Central Google Scholar
Martens, J.H. et al. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J.24, 800–812 (2005). CASPubMedPubMed Central Google Scholar
Bilodeau, S., Kagey, M.H., Frampton, G.M., Rahl, P.B. & Young, R.A. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev.23, 2484–2489 (2009). CASPubMedPubMed Central Google Scholar
Lohmann, F. et al. KMT1E mediated H3K9 methylation is required for the maintenance of embryonic stem cells by repressing trophectoderm differentiation. Stem Cells28, 201–212 (2010). CASPubMed Google Scholar
Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet.39, 457–466 (2007). CASPubMed Google Scholar
Cedar, H. & Bergman, Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet.10, 295–304 (2009). CASPubMed Google Scholar
Mikkelsen, T.S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature454, 49–55 (2008). CASPubMedPubMed Central Google Scholar
Imamura, M. et al. Transcriptional repression and DNA hypermethylation of a small set of ES cell marker genes in male germline stem cells. BMC Dev. Biol.6, 34 (2006). PubMedPubMed Central Google Scholar
Ramsahoye, B.H. et al. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl. Acad. Sci. USA97, 5237–5242 (2000). CASPubMedPubMed Central Google Scholar
Haines, T.R., Rodenhiser, D.I. & Ainsworth, P.J. Allele-specific non-CpG methylation of the Nf1 gene during early mouse development. Dev. Biol.240, 585–598 (2001). CASPubMed Google Scholar
Dodge, J.E., Ramsahoye, B.H., Wo, Z.G., Okano, M. & Li, E. De novo methylation of MMLV provirus in embryonic stem cells: CpG versus non-CpG methylation. Gene289, 41–48 (2002). CASPubMed Google Scholar
Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature452, 215–219 (2008). CASPubMedPubMed Central Google Scholar
Chan, S.W., Henderson, I.R. & Jacobsen, S.E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet.6, 351–360 (2005). CASPubMed Google Scholar
Lomvardas, S. et al. Interchromosomal interactions and olfactory receptor choice. Cell126, 403–413 (2006). CASPubMed Google Scholar
Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science324, 930–935 (2009). CASPubMedPubMed Central Google Scholar
Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science324, 929–930 (2009). CASPubMedPubMed Central Google Scholar
Ito, S. et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature466, 1129–1133 (2010). CASPubMedPubMed Central Google Scholar
Down, T.A. et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol.26, 779–785 (2008). CASPubMedPubMed Central Google Scholar
Wu, S.C. & Zhang, Y. Active DNA demethylation: many roads lead to Rome. Nat. Rev. Mol. Cell Biol.11, 607–620 (2010). CASPubMedPubMed Central Google Scholar
Jeltsch, A. Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. ChemBioChem3, 274–293 (2002). CASPubMed Google Scholar
Guenther, M.G., Levine, S.S., Boyer, L.A., Jaenisch, R. & Young, R.A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell130, 77–88 (2007). CASPubMedPubMed Central Google Scholar
Heintzman, N.D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet.39, 311–318 (2007). CASPubMed Google Scholar
Boiani, M. & Scholer, H.R. Regulatory networks in embryo-derived pluripotent stem cells. Nat. Rev. Mol. Cell Biol.6, 872–884 (2005). CASPubMed Google Scholar
Xie, W. et al. Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Mol. Cell33, 417–427 (2009). CASPubMedPubMed Central Google Scholar
Daujat, S. et al. H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming. Nat. Struct. Mol. Biol.16, 777–781 (2009). CASPubMed Google Scholar
Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat. Methods7, 133–136 (2010). CASPubMedPubMed Central Google Scholar
Goren, A. et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat. Methods7, 47–49 (2010). CASPubMed Google Scholar
Xu, J. et al. Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes Dev.23, 2824–2838 (2009). CASPubMedPubMed Central Google Scholar
Epsztejn-Litman, S. et al. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat. Struct. Mol. Biol.15, 1176–1183 (2008). CASPubMedPubMed Central Google Scholar
Feldman, N. et al. G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat. Cell Biol.8, 188–194 (2006). CASPubMed Google Scholar
Cherry, S.R., Biniszkiewicz, D., van Parijs, L., Baltimore, D. & Jaenisch, R. Retroviral expression in embryonic stem cells and hematopoietic stem cells. Mol. Cell. Biol.20, 7419–7426 (2000). CASPubMedPubMed Central Google Scholar
Matsui, T. et al. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature464, 927–931 (2010). CASPubMed Google Scholar
Sen, G.L., Reuter, J.A., Webster, D.E., Zhu, L. & Khavari, P.A. DNMT1 maintains progenitor function in self-renewing somatic tissue. Nature463, 563–567 (2010). CASPubMedPubMed Central Google Scholar
Bröske, A.M. et al. DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat. Genet.41, 1207–1215 (2009). PubMed Google Scholar
Trowbridge, J.J., Snow, J.W., Kim, J. & Orkin, S.H. DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells. Cell Stem Cell5, 442–449 (2009). CASPubMedPubMed Central Google Scholar
Ji, H. et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature467, 338–342 (2010). CASPubMedPubMed Central Google Scholar
Tadokoro, Y., Ema, H., Okano, M., Li, E. & Nakauchi, H. De novo DNA methyltransferase is essential for self-renewal, but not for differentiation, in hematopoietic stem cells. J. Exp. Med.204, 715–722 (2007). CASPubMedPubMed Central Google Scholar
Jacobs, J.J., Kieboom, K., Marino, S., DePinho, R.A. & van Lohuizen, M. The oncogene and Polycomb-group gene bmi-1 regulates cell proliferation and senescence through the ink4a locus. Nature397, 164–168 (1999). CASPubMed Google Scholar
Woo, C.J., Kharchenko, P.V., Daheron, L., Park, P.J. & Kingston, R.E. A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell140, 99–110 (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
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
Shen, X. et al. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell139, 1303–1314 (2009). PubMedPubMed Central Google Scholar
Khalil, A.M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA106, 11667–11672 (2009). CASPubMedPubMed Central Google Scholar
Gupta, R.A. et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature464, 1071–1076 (2010). CASPubMedPubMed Central Google Scholar
Hochedlinger, K. & Jaenisch, R. Nuclear reprogramming and pluripotency. Nature441, 1061–1067 (2006). CASPubMed Google Scholar
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell126, 663–676 (2006). 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
Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell131, 861–872 (2007). CASPubMed Google Scholar
Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science318, 1917–1920 (2007). CASPubMed Google Scholar
Maherali, N. et al. Global epigenetic remodeling in directly reprogrammed fibroblasts. Cell Stem Cell1, 55–70 (2007). CASPubMed Google Scholar
Meissner, A., Wernig, M. & Jaenisch, R. Direct reprogramming of genetically unmodified fibroblasts into pluripotent stem cells. Nat. Biotechnol.25, 1177–1181 (2007). CASPubMed Google Scholar
Wernig, M. et al. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature448, 318–324 (2007). CASPubMed Google Scholar
Huangfu, D. et al. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat. Biotechnol.26, 795–797 (2008). CASPubMedPubMed Central Google Scholar
Ichida, J.K. et al. A small-molecule inhibitor of tgf-Beta signaling replaces sox2 in reprogramming by inducing nanog. Cell Stem Cell5, 491–503 (2009). CASPubMedPubMed Central Google Scholar
Chin, M.H. et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell5, 111–123 (2009). CASPubMedPubMed Central Google Scholar
Polo, J.M. et al. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nat. Biotechnol.28, 848–855 (2010). CASPubMedPubMed Central Google Scholar
Ng, R.K. & Gurdon, J.B. Epigenetic memory of active gene transcription is inherited through somatic cell nuclear transfer. Proc. Natl. Acad. Sci. USA102, 1957–1962 (2005). CASPubMedPubMed Central Google Scholar
Ng, R.K. & Gurdon, J.B. Epigenetic memory of an active gene state depends on histone H3.3 incorporation into chromatin in the absence of transcription. Nat. Cell Biol.10, 102–109 (2008). CASPubMed Google Scholar
Tamashiro, K.L. et al. Cloned mice have an obese phenotype not transmitted to their offspring. Nat. Med.8, 262–267 (2002). CASPubMed Google Scholar
Bortvin, A. et al. Incomplete reactivation of Oct4-related genes in mouse embryos cloned from somatic nuclei. Development130, 1673–1680 (2003). CASPubMed Google Scholar
Blelloch, R. et al. Reprogramming efficiency following somatic cell nuclear transfer is influenced by the differentiation and methylation state of the donor nucleus. Stem Cells24, 2007–2013 (2006). CASPubMedPubMed Central Google Scholar
Hotchkiss, R.D. The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. J. Biol. Chem.175, 315–332 (1948). CASPubMed Google Scholar
Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature409, 860–921 (2001). CASPubMed Google Scholar
Heintzman, N.D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet.39, 311–318 (2007). CASPubMed Google Scholar
Marson, A. et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell134, 521–533 (2008). CASPubMedPubMed Central Google Scholar
Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature458, 223–227 (2009). CASPubMedPubMed Central Google Scholar
Khalil, A.M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA106, 11667–11672 (2009). CASPubMedPubMed Central Google Scholar