Hirabayashi, Y. & Gotoh, Y. Stage-dependent fate determination of neural precursor cells in mouse forebrain. Neurosci. Res.51, 331–336 (2005). ArticleCASPubMed Google Scholar
Molyneaux, B. J., Arlotta, P., Menezes, J. R. & Macklis, J. D. Neuronal subtype specification in the cerebral cortex. Nature Rev. Neurosci.8, 427–437 (2007). ArticleCAS Google Scholar
Frantz, G. D. & McConnell, S. K. Restriction of late cerebral cortical progenitors to an upper-layer fate. Neuron17, 55–61 (1996). This study showed that, late in development, neocortical NPCs lose the capacity to generate neurons that are normally generated at an earlier stage, possibly owing to a cell-intrinsic mechanism. ArticleCASPubMed Google Scholar
Desai, A. R. & McConnell, S. K. Progressive restriction in fate potential by neural progenitors during cerebral cortical development. Development127, 2863–2872 (2000). ArticleCASPubMed Google Scholar
Borrelli, E., Nestler, E. J., Allis, C. D. & Sassone-Corsi, P. Decoding the epigenetic language of neuronal plasticity. Neuron60, 961–974 (2008). ArticleCASPubMedPubMed Central Google Scholar
Mehler, M. F. Epigenetic principles and mechanisms underlying nervous system functions in health and disease. Prog. Neurobiol.86, 305–341 (2008). ArticleCASPubMedPubMed Central Google Scholar
Copray, S., Huynh, J. L., Sher, F., Casaccia-Bonnefil, P. & Boddeke, E. Epigenetic mechanisms facilitating oligodendrocyte development, maturation, and aging. Glia57, 1579–1587 (2009). ArticlePubMedPubMed Central Google Scholar
Boyer, L. A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature441, 349–353 (2006). ArticleCASPubMed Google Scholar
Lee, T. I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell125, 301–313 (2006). References 11 and 12 identified a large set of PcG target genes, which are enriched for genes that control development and transcription in ESCs. See also reference 105. ArticleCASPubMedPubMed Central Google Scholar
Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet.4, e1000242 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Endoh, M. et al. Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity. Development135, 1513–1524 (2008). ArticleCASPubMed Google Scholar
Azuara, V. et al. Chromatin signatures of pluripotent cell lines. Nature Cell Biol.8, 532–538 (2006). ArticleCASPubMed Google Scholar
Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell125, 315–326 (2006). References 15 and 16 showed that key genes for development are poised for activation in ESCs by the combination of histone modifications H3K27me3 and H3K4me3. ArticleCASPubMed 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). ArticleCASPubMed Google Scholar
Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature448, 553–560 (2007). This study used ChIP–seq technology to describe the genome-wide histone modification state of mouse ESCs, NPCs and embryonic fibroblasts. ArticleCASPubMedPubMed 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). An important study tracking genome-wide epigenetic modification by PcG proteins and DNA methylation during differentiation of ESCs to neural progenitors and to terminally differentiated neurons. ArticleCASPubMed Google Scholar
Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature454, 766–770 (2008). This study provided the first genome-wide DNA methylation profile at nucleotide resolution in ESCs, ESC-derived NPCs and other primary tissues. ArticleCASPubMedPubMed Central Google Scholar
Fouse, S. D. 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). ArticleCASPubMedPubMed Central Google Scholar
Chong, J. A. et al. REST: a mammalian silencer protein that restricts sodium channel gene expression to neurons. Cell80, 949–957 (1995). ArticleCASPubMed Google Scholar
Schoenherr, C. J. & Anderson, D. J. The neuron-restrictive silencer factor (NRSF): a coordinate repressor of multiple neuron-specific genes. Science267, 1360–1363 (1995). ArticleCASPubMed Google Scholar
Lunyak, V. V. et al. Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science298, 1747–1752 (2002). ArticleCASPubMed Google Scholar
Ballas, N. & Mandel, G. The many faces of REST oversee epigenetic programming of neuronal genes. Curr. Opin. Neurobiol.15, 500–506 (2005). ArticleCASPubMed Google Scholar
Ballas, N., Grunseich, C., Lu, D. D., Speh, J. C. & Mandel, G. REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis. Cell121, 645–657 (2005). This study showed the roles of REST in long-term repression in terminally differentiated fibroblasts and in short-term repression in ESCs or neural progenitors. ArticleCASPubMed Google Scholar
Singh, S. K., Kagalwala, M. N., Parker-Thornburg, J., Adams, H. & Majumder, S. REST maintains self-renewal and pluripotency of embryonic stem cells. Nature453, 223–227 (2008). ArticleCASPubMedPubMed Central Google Scholar
Jorgensen, H. F. et al. REST selectively represses a subset of RE1-containing neuronal genes in mouse embryonic stem cells. Development136, 715–721 (2009). ArticleCASPubMedPubMed Central Google Scholar
Loh, Y. H. et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nature Genet.38, 431–440 (2006). CASPubMed Google Scholar
Jørgensen, H. F., Chen, Z. F., Merkenschlager, M. & Fisher, A. G. Is REST required for ESC pluripotency? Nature457, E4–E5; discussion E7 (2009). ArticleCAS Google Scholar
Buckley, N. J., Johnson, R., Sun, Y. M. & Stanton, L. W. Is REST a regulator of pluripotency? Nature457, E5–E6; discussion E7 (2009). ArticleCAS Google Scholar
Shi, Y. et al. Coordinated histone modifications mediated by a CtBP co-repressor complex. Nature422, 735–738 (2003). ArticleCASPubMed Google Scholar
Roopra, A., Qazi, R., Schoenike, B., Daley, T. J. & Morrison, J. F. Localized domains of G9a-mediated histone methylation are required for silencing of neuronal genes. Mol. Cell14, 727–738 (2004). ArticleCASPubMed Google Scholar
Tahiliani, M. et al. The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation. Nature447, 601–605 (2007). ArticleCASPubMed Google Scholar
Iwase, S. et al. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell128, 1077–1088 (2007). ArticleCASPubMed Google Scholar
Reik, W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature447, 425–432 (2007). ArticleCASPubMed Google Scholar
Schoeftner, S. & Blasco, M. A. A 'higher order' of telomere regulation: telomere heterochromatin and telomeric RNAs. EMBO J.28, 2323–2336 (2009). ArticleCASPubMedPubMed Central Google Scholar
Lee, E. R., Murdoch, F. E. & Fritsch, M. K. High histone acetylation and decreased polycomb repressive complex 2 member levels regulate gene specific transcriptional changes during early embryonic stem cell differentiation induced by retinoic acid. Stem Cells25, 2191–2199 (2007). ArticleCASPubMed Google Scholar
Hirabayashi, Y. et al. Polycomb limits the neurogenic competence of neural precursor cells to promote astrogenic fate transition. Neuron63, 600–613 (2009). This paper shows that PcG proteins restrict the neurogenic potential of NPCs in the late stage of neocortical development and cause the developmental-stage-dependent fate switch. ArticleCASPubMed Google Scholar
Golebiewska, A., Atkinson, S. P., Lako, M. & Armstrong, L. Epigenetic landscaping during hESC differentiation to neural cells. Stem Cells27, 1298–1308 (2009). ArticleCASPubMed Google Scholar
Wen, B., Wu, H., Shinkai, Y., Irizarry, R. A. & Feinberg, A. P. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nature Genetics41, 246–250 (2009). ArticleCASPubMedPubMed Central Google Scholar
Westbrook, T. F. et al. SCFβ-TRCP controls oncogenic transformation and neural differentiation through REST degradation. Nature452, 370–374 (2008). ArticleCASPubMedPubMed Central Google Scholar
Ringrose, L. & Paro, R. Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development134, 223–232 (2007). ArticleCASPubMed Google Scholar
Schuettengruber, B. & Cavalli, G. Recruitment of polycomb group complexes and their role in the dynamic regulation of cell fate choice. Development136, 3531–3542 (2009). ArticleCASPubMed Google Scholar
Sing, A. et al. A vertebrate Polycomb response element governs segmentation of the posterior hindbrain. Cell138, 885–897 (2009). ArticleCASPubMed 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). ArticleCASPubMedPubMed Central Google Scholar
Lan, F., Nottke, A. C. & Shi, Y. Mechanisms involved in the regulation of histone lysine demethylases. Curr. Opin. Cell Biol.20, 316–325 (2008). ArticleCASPubMedPubMed Central Google Scholar
Ma, D. K., Guo, J. U., Ming, G. L. & Song, H. DNA excision repair proteins and Gadd45 as molecular players for active DNA demethylation. Cell Cycle8, 1526–1531 (2009). ArticleCASPubMed Google Scholar
Walsh, C. & Cepko, C. L. Widespread dispersion of neuronal clones across functional regions of the cerebral cortex. Science255, 434–440 (1992). ArticleCASPubMed Google Scholar
Noctor, S. C., Martinez-Cerdeno, V. & Kriegstein, A. R. Distinct behaviors of neural stem and progenitor cells underlie cortical neurogenesis. J. Comp. Neurol.508, 28–44 (2008). ArticlePubMedPubMed Central Google Scholar
Costa, M. R., Bucholz, O., Schroeder, T. & Gotz, M. Late origin of glia-restricted progenitors in the developing mouse cerebral cortex. Cereb. Cortex19, i135–i143 (2009). ArticlePubMed Google Scholar
Qian, X. et al. Timing of CNS cell generation: a programmed sequence of neuron and glial cell production from isolated murine cortical stem cells. Neuron28, 69–80 (2000). ArticleCASPubMed Google Scholar
Shen, Q. et al. The timing of cortical neurogenesis is encoded within lineages of individual progenitor cells. Nature Neurosci.9, 743–751 (2006). References 56 and 57 show that isolated mouse cortical stem cells grown in clonal cultures recapitulated the sequential generation of early-born neurons, late-born neurons and glia that is observedin vivo . ArticleCASPubMed Google Scholar
Mizutani, K. & Saito, T. Progenitors resume generating neurons after temporary inhibition of neurogenesis by Notch activation in the mammalian cerebral cortex. Development132, 1295–1304 (2005). ArticleCASPubMed Google Scholar
McConnell, S. K. & Kaznowski, C. E. Cell cycle dependence of laminar determination in developing neocortex. Science254, 282–285 (1991). ArticleCASPubMed Google Scholar
Johe, K. K., Hazel, T. G., Muller, T., Dugich-Djordjevic, M. M. & McKay, R. D. Single factors direct the differentiation of stem cells from the fetal and adult central nervous system. Genes Dev.10, 3129–3140 (1996). The authors established anin vitrosystem to culture NPCs and identified extracellular factors that direct lineage commitment, enabling analysis of the differentiation capacity of a given NPC. ArticleCASPubMed Google Scholar
He, F. et al. A positive autoregulatory loop of Jak–STAT signaling controls the onset of astrogliogenesis. Nature Neurosci.8, 616–625 (2005). ArticleCASPubMed Google Scholar
Bonni, A. et al. Regulation of gliogenesis in the central nervous system by the JAK–STAT signaling pathway. Science278, 477–483 (1997). ArticleCASPubMed Google Scholar
Barnabe-Heider, F. et al. Evidence that embryonic neurons regulate the onset of cortical gliogenesis via cardiotrophin-1. Neuron48, 253–265 (2005). ArticleCASPubMed Google Scholar
Yoshimatsu, T. et al. Non-cell-autonomous action of STAT3 in maintenance of neural precursor cells in the mouse neocortex. Development133, 2553–2563 (2006). ArticleCASPubMed Google Scholar
Derouet, D. et al. Neuropoietin, a new IL-6-related cytokine signaling through the ciliary neurotrophic factor receptor. Proc. Natl Acad. Sci. USA101, 4827–4832 (2004). ArticleCASPubMedPubMed Central Google Scholar
Uemura, A. et al. Cardiotrophin-like cytokine induces astrocyte differentiation of fetal neuroepithelial cells via activation of STAT3. Cytokine18, 1–7 (2002). ArticleCASPubMed Google Scholar
Song, M. R. & Ghosh, A. FGF2-induced chromatin remodeling regulates CNTF-mediated gene expression and astrocyte differentiation. Nature Neurosci.7, 229–235 (2004). ArticlePubMedCAS Google Scholar
Takizawa, T. et al. DNA methylation is a critical cell-intrinsic determinant of astrocyte differentiation in the fetal brain. Dev. Cell1, 749–758 (2001). ArticleCASPubMed Google Scholar
Molne, M. et al. Early cortical precursors do not undergo LIF-mediated astrocytic differentiation. J. Neurosci. Res.59, 301–311 (2000). ArticleCASPubMed Google Scholar
Fan, G. et al. DNA methylation controls the timing of astrogliogenesis through regulation of JAK–STAT signaling. Development132, 3345–3356 (2005). References 69 and 71 showed that DNA methylation at gene regulatory elements of GFAP and JAK–STAT pathway components block astrocytic differentiation in early neocortical development. ArticleCASPubMed Google Scholar
Namihira, M., Nakashima, K. & Taga, T. Developmental stage dependent regulation of DNA methylation and chromatin modification in a immature astrocyte specific gene promoter. FEBS Lett.572, 184–188 (2004). ArticleCASPubMed Google Scholar
Teter, B., Finch, C. E. & Condorelli, D. F. DNA methylation in the glial fibrillary acidic protein gene: map of CpG methylation sites and summary of analysis by restriction enzymes and by LMPCR. J. Neurosci. Res.39, 708–709 (1994). ArticleCASPubMed Google Scholar
Namihira, M. et al. Committed neuronal precursors confer astrocytic potential on residual neural precursor cells. Dev. Cell16, 245–255 (2009). ArticleCASPubMed Google Scholar
Naka, H., Nakamura, S., Shimazaki, T. & Okano, H. Requirement for COUP-TFI and II in the temporal specification of neural stem cells in CNS development. Nature Neurosci.11, 1014–1023 (2008). ArticleCASPubMed Google Scholar
Setoguchi, H. et al. Methyl-CpG binding proteins are involved in restricting differentiation plasticity in neurons. J. Neurosci. Res.84, 969–979 (2006). ArticleCASPubMed Google Scholar
Kohyama, J. et al. Epigenetic regulation of neural cell differentiation plasticity in the adult mammalian brain. Proc. Natl Acad. Sci. USA105, 18012–18017 (2008). ArticleCASPubMedPubMed Central Google Scholar
Hirabayashi, Y. et al. The Wnt/β-catenin pathway directs neuronal differentiation of cortical neural precursor cells. Development131, 2791–2801 (2004). ArticleCASPubMed Google Scholar
Muroyama, Y., Kondoh, H. & Takada, S. Wnt proteins promote neuronal differentiation in neural stem cell culture. Biochem. Biophys. Res. Commun.313, 915–921 (2004). ArticleCASPubMed Google Scholar
Israsena, N., Hu, M., Fu, W., Kan, L. & Kessler, J. A. The presence of FGF2 signaling determines whether β-catenin exerts effects on proliferation or neuronal differentiation of neural stem cells. Dev. Biol.268, 220–231 (2004). ArticleCASPubMed Google Scholar
Zhou, C. J., Borello, U., Rubenstein, J. L. & Pleasure, S. J. Neuronal production and precursor proliferation defects in the neocortex of mice with loss of function in the canonical Wnt signaling pathway. Neuroscience142, 1119–1131 (2006). ArticleCASPubMed Google Scholar
Lyu, J., Yamamoto, V. & Lu, W. Cleavage of the Wnt receptor Ryk regulates neuronal differentiation during cortical neurogenesis. Dev. Cell15, 773–780 (2008). ArticleCASPubMed Google Scholar
Ivaniutsin, U., Chen, Y., Mason, J. O., Price, D. J. & Pratt, T. Adenomatous polyposis coli is required for early events in the normal growth and differentiation of the developing cerebral cortex. Neural Dev.4, 3 (2009). ArticlePubMedPubMed CentralCAS Google Scholar
Guillemot, F. Cell fate specification in the mammalian telencephalon. Prog. Neurobiol.83, 37–52 (2007). ArticleCASPubMed Google Scholar
Guillemot, F. Cellular and molecular control of neurogenesis in the mammalian telencephalon. Curr. Opin. Cell Biol.17, 639–647 (2005). ArticleCASPubMed Google Scholar
Sun, Y. et al. Neurogenin promotes neurogenesis and inhibits glial differentiation by independent mechanisms. Cell104, 365–376 (2001). ArticleCASPubMed Google Scholar
Roman-Trufero, M. et al. Maintenance of undifferentiated state and self-renewal of embryonic neural stem cells by Polycomb protein Ring1B. Stem Cells27, 1559–1570 (2009). ArticleCASPubMed Google Scholar
Molofsky, A. V. et al. Bmi-1 dependence distinguishes neural stem cell self-renewal from progenitor proliferation. Nature425, 962–967 (2003). ArticleCASPubMedPubMed Central Google Scholar
Fasano, C. A. et al. shRNA knockdown of Bmi-1 reveals a critical role for p21-Rb pathway in NSC self-renewal during development. Cell Stem Cell1, 87–99 (2007). ArticleCASPubMed Google Scholar
He, S. et al. Bmi-1 over-expression in neural stem/progenitor cells increases proliferation and neurogenesis in culture but has little effect on these functions in vivo. Dev. Biol.328, 257–272 (2009). ArticleCASPubMedPubMed Central Google Scholar
Fasano, C. A. et al. Bmi-1 cooperates with Foxg1 to maintain neural stem cell self-renewal in the forebrain. Genes Dev.23, 561–574 (2009). ArticleCASPubMedPubMed Central Google Scholar
Lessard, J. et al. Functional antagonism of the _Polycomb_-Group genes eed and Bmi1 in hemopoietic cell proliferation. Genes Dev.13, 2691–2703 (1999). ArticleCASPubMedPubMed Central Google Scholar
Pietersen, A. M. et al. EZH2 and BMI1 inversely correlate with prognosis and TP53 mutation in breast cancer. Breast Cancer Res.10, R109 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Kessaris, N. et al. Competing waves of oligodendrocytes in the forebrain and postnatal elimination of an embryonic lineage. Nature Neurosci.9, 173–179 (2006). ArticleCASPubMed Google Scholar
Petryniak, M. A., Potter, G. B., Rowitch, D. H. & Rubenstein, J. L. Dlx1 and Dlx2 control neuronal versus oligodendroglial cell fate acquisition in the developing forebrain. Neuron55, 417–433 (2007). ArticleCASPubMedPubMed Central Google Scholar
Lim, D. A. et al. Chromatin remodelling factor Mll1 is essential for neurogenesis from postnatal neural stem cells. Nature458, 529–533 (2009). This work showed that the TrxG member MLL is required for resolution of the bivalent state of theDlx2locus and for neurogenesis in the postnatal brain. ArticleCASPubMedPubMed Central Google Scholar
Sher, F. et al. Differentiation of neural stem cells into oligodendrocytes: involvement of the polycomb group protein Ezh2. Stem Cells26, 2875–2883 (2008). ArticleCASPubMed Google Scholar
Barres, B. A., Lazar, M. A. & Raff, M. C. A novel role for thyroid hormone, glucocorticoids and retinoic acid in timing oligodendrocyte development. Development120, 1097–1108 (1994). ArticleCASPubMed Google Scholar
Mabie, P. C. et al. Bone morphogenetic proteins induce astroglial differentiation of oligodendroglial-astroglial progenitor cells. J. Neurosci.17, 4112–4120 (1997). ArticleCASPubMedPubMed Central Google Scholar
Kondo, T. & Raff, M. Oligodendrocyte precursor cells reprogrammed to become multipotential CNS stem cells. Science289, 1754–1757 (2000). ArticleCASPubMed Google Scholar
Kondo, T. & Raff, M. Chromatin remodeling and histone modification in the conversion of oligodendrocyte precursors to neural stem cells. Genes Dev.18, 2963–2972 (2004). References 100 and 101 showed that chromatin remodelling is involved in the reprogramming of lineage-committed oligodendrocytes into multipotent NPCs. ArticleCASPubMedPubMed Central Google Scholar
Lyssiotis, C. A. et al. Inhibition of histone deacetylase activity induces developmental plasticity in oligodendrocyte precursor cells. Proc. Natl Acad. Sci. USA104, 14982–14987 (2007). ArticleCASPubMedPubMed Central Google Scholar
Liu, A. et al. The glial or neuronal fate choice of oligodendrocyte progenitors is modulated by their ability to acquire an epigenetic memory. J. Neurosci.27, 7339–7343 (2007). ArticleCASPubMedPubMed Central 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). ArticleCASPubMedPubMed Central Google Scholar
Schwartz, Y. B. & Pirrotta, V. Polycomb silencing mechanisms and the management of genomic programmes. Nature Rev. Genet.8, 9–22 (2007). ArticleCASPubMed Google Scholar
Maherali, N. et al. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell1, 55–70 (2007). ArticleCASPubMed Google Scholar
Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature454, 49–55 (2008). This study describes gene expression profiling and chromatin-state maps of fully and partially reprogrammed cell lines; treatment with DNMT inhibitors was found to improve the efficiency of reprogramming. ArticleCASPubMedPubMed Central Google Scholar
Gurdon, J. B. The developmental capacity of nuclei taken from intestinal epithelium cells of feeding tadpoles. J. Embryol. Exp. Morphol.10, 622–640 (1962). 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). ArticleCASPubMed Google Scholar
Okita, K., Ichisaka, T. & Yamanaka, S. Generation of germline-competent induced pluripotent stem cells. Nature448, 313–317 (2007). ArticleCASPubMed Google Scholar
Stadtfeld, M., Brennand, K. & Hochedlinger, K. Reprogramming of pancreatic beta cells into induced pluripotent stem cells. Curr. Biol.18, 890–894 (2008). ArticleCASPubMedPubMed Central Google Scholar
Kim, J. B. et al. Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors. Nature454, 646–650 (2008). ArticleCASPubMed Google Scholar
Kim, J. B. et al. Oct4-induced pluripotency in adult neural stem cells. Cell136, 411–419 (2009). ArticleCASPubMed Google Scholar
Kim, J. B. et al. Direct reprogramming of human neural stem cells by OCT4. Nature461, 649–653 (2009). ArticleCASPubMed Google Scholar
Shi, Y. et al. A combined chemical and genetic approach for the generation of induced pluripotent stem cells. Cell Stem Cell2, 525–528 (2008). ArticleCASPubMed Google Scholar
Huangfu, D. et al. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nature Biotech.26, 795–797 (2008). ArticleCAS Google Scholar
Trojer, P. & Reinberg, D. Facultative heterochromatin: is there a distinctive molecular signature? Mol. Cell28, 1–13 (2007). ArticleCASPubMed Google Scholar
Li, E. Chromatin modification and epigenetic reprogramming in mammalian development. Nature Rev. Genet.3, 662–673 (2002). ArticleCASPubMed Google Scholar
Barreto, G. et al. Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature445, 671–675 (2007). ArticleCASPubMed Google Scholar
Rai, K. et al. DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and Gadd45. Cell135, 1201–1212 (2008). ArticleCASPubMedPubMed Central Google Scholar
Martin, C. & Zhang, Y. The diverse functions of histone lysine methylation. Nature Rev. Mol. Cell Biol.6, 838–849 (2005). ArticleCAS Google Scholar
Tachibana, M. et al. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev.16, 1779–1791 (2002). ArticleCASPubMedPubMed Central Google Scholar
Rice, J. C. et al. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell12, 1591–1598 (2003). ArticleCASPubMed Google Scholar
Loyola, A. et al. The HP1α–CAF1–SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin. EMBO Rep.10, 769–775 (2009). ArticleCASPubMedPubMed Central Google Scholar
Epsztejn-Litman, S. et al. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nature Struct. Mol. Biol.15, 1176–1183 (2008). ArticleCAS Google Scholar
Peters, A. H. et al. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell107, 323–337 (2001). ArticleCASPubMed Google Scholar
Klose, R. J. & Zhang, Y. Regulation of histone methylation by demethylimination and demethylation. Nature Rev. Mol. Cell Biol.8, 307–318 (2007). ArticleCAS Google Scholar
Whetstine, J. R. et al. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell125, 467–481 (2006). ArticleCASPubMed Google Scholar
Fodor, B. D. et al. Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev.20, 1557–1562 (2006). ArticleCASPubMedPubMed Central Google Scholar
Wissmann, M. et al. Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nature Cell Biol.9, 347–353 (2007). ArticleCASPubMed Google Scholar
Cao, R. & Zhang, Y. The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3. Curr. Opin. Genet. Dev.14, 155–164 (2004). ArticleCASPubMed 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, 491–502 (2008). ArticleCASPubMedPubMed Central Google Scholar
Kalantry, S. et al. The Polycomb group protein Eed protects the inactive X-chromosome from differentiation-induced reactivation. Nature Cell Biol.8, 195–202 (2006). ArticleCASPubMed Google Scholar
Umlauf, D. et al. Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes. Nature Genet.36, 1296–1300 (2004). ArticleCASPubMed Google Scholar
Mager, J., Montgomery, N. D., de Villena, F. P. & Magnuson, T. Genome imprinting regulated by the mouse Polycomb group protein Eed. Nature Genet.33, 502–507 (2003). ArticleCASPubMed Google Scholar
van Driel, R., Fransz, P. F. & Verschure, P. J. The eukaryotic genome: a system regulated at different hierarchical levels. J. Cell Sci.116, 4067–4075 (2003). ArticleCASPubMed Google Scholar
Misteli, T. Beyond the sequence: cellular organization of genome function. Cell128, 787–800 (2007). ArticleCASPubMed Google Scholar
Williams, R. R. et al. Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus. J. Cell Sci.119, 132–140 (2006). ArticleCASPubMed Google Scholar
Kosak, S. T. & Groudine, M. Form follows function: the genomic organization of cellular differentiation. Genes Dev.18, 1371–1384 (2004). ArticleCASPubMed Google Scholar
Perry, P. et al. A dynamic switch in the replication timing of key regulator genes in embryonic stem cells upon neural induction. Cell Cycle3, 1645–1650 (2004). ArticleCASPubMed Google Scholar
Hiratani, I., Takebayashi, S., Lu, J. & Gilbert, D. M. Replication timing and transcriptional control: beyond cause and effect — part II. Curr. Opin. Genet. Dev.19, 142–149 (2009). ArticleCASPubMedPubMed Central Google Scholar
Hiratani, I. et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol.6, e245 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Lee, S. & Lee, S. K. Crucial roles of histone-modifying enzymes in mediating neural cell-type specification. Curr. Opin. Neurobiol.20, 29–36 (2010). ArticleCASPubMedPubMed Central Google Scholar
Shahbazian, M. D. & Grunstein, M. Functions of site-specific histone acetylation and deacetylation. Annu. Rev. Biochem.76, 75–100 (2007). ArticleCASPubMed Google Scholar
Hsieh, J., Nakashima, K., Kuwabara, T., Mejia, E. & Gage, F. H. Histone deacetylase inhibition-mediated neuronal differentiation of multipotent adult neural progenitor cells. Proc. Natl Acad. Sci. USA101, 16659–16664 (2004). ArticleCASPubMedPubMed Central Google Scholar
Yu, I. T. et al. Valproic acid promotes neuronal differentiation by induction of proneural factors in association with H4 acetylation. Neuropharmacology56, 473–480 (2009). ArticleCASPubMed Google Scholar
Montgomery, R. L., Hsieh, J., Barbosa, A. C., Richardson, J. A. & Olson, E. N. Histone deacetylases 1 and 2 control the progression of neural precursors to neurons during brain development. Proc. Natl Acad. Sci. USA106, 7876–7881 (2009). ArticleCASPubMedPubMed Central Google Scholar
Shaked, M. et al. Histone deacetylases control neurogenesis in embryonic brain by inhibition of BMP2/4 signaling. PLoS ONE3, e2668 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Koyano-Nakagawa, N., Wettstein, D. & Kintner, C. Activation of Xenopus genes required for lateral inhibition and neuronal differentiation during primary neurogenesis. Mol. Cell. Neurosci.14, 327–339 (1999). ArticleCASPubMed Google Scholar
Lee, S., Lee, B., Lee, J. W. & Lee, S. K. Retinoid signaling and Neurogenin2 function are coupled for the specification of spinal motor neurons through a chromatin modifier CBP. Neuron62, 641–654 (2009). ArticleCASPubMedPubMed Central Google Scholar
Nakashima, K. et al. Synergistic signaling in fetal brain by STAT3–Smad1 complex bridged by p300. Science284, 479–482 (1999). ArticleCASPubMed Google Scholar
Jepsen, K. et al. SMRT-mediated repression of an H3K27 demethylase in progression from neural stem cell to neuron. Nature450, 415–419 (2007). ArticleCASPubMed Google Scholar
Hermanson, O., Jepsen, K. & Rosenfeld, M. G. N-CoR controls differentiation of neural stem cells into astrocytes. Nature419, 934–939 (2002). ArticleCASPubMed Google Scholar
Clapier, C. R. & Cairns, B. R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem.78, 273–304 (2009). ArticleCASPubMed Google Scholar
Seo, S., Richardson, G. A. & Kroll, K. L. The SWI/SNF chromatin remodeling protein Brg1 is required for vertebrate neurogenesis and mediates transactivation of Ngn and NeuroD. Development132, 105–115 (2005). ArticleCASPubMed Google Scholar
Lessard, J. et al. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron55, 201–215 (2007). ArticleCASPubMedPubMed Central Google Scholar
Waddington, C. H. The Strategy of the Genes. (Allen and Unwin, London, 1957). Google Scholar
Tzouanacou, E., Wegener, A., Wymeersch, F. J., Wilson, V. & Nicolas, J. F. Redefining the progression of lineage segregations during mammalian embryogenesis by clonal analysis. Dev. Cell17, 365–376 (2009). ArticleCASPubMed Google Scholar
Yuan, P. et al. Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. Genes Dev.23, 2507–2520 (2009). ArticleCASPubMedPubMed Central Google Scholar
Bilodeau, S. et al. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev.23, 2484–2489 (2009). ArticleCASPubMedPubMed Central Google Scholar