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• W2017050785 abstract "Embryonic stem cells and induced pluripotent stem cells hold great promise for regenerative medicine. These cells can be propagated in culture in an undifferentiated state but can be induced to differentiate into specialized cell types. Moreover, these cells provide a powerful model system for studies of cellular identity and early mammalian development. Recent studies have provided insights into the transcriptional control of embryonic stem cell state, including the regulatory circuitry underlying pluripotency. These studies have, as a consequence, uncovered fundamental mechanisms that control mammalian gene expression, connect gene expression to chromosome structure, and contribute to human disease. Embryonic stem cells and induced pluripotent stem cells hold great promise for regenerative medicine. These cells can be propagated in culture in an undifferentiated state but can be induced to differentiate into specialized cell types. Moreover, these cells provide a powerful model system for studies of cellular identity and early mammalian development. Recent studies have provided insights into the transcriptional control of embryonic stem cell state, including the regulatory circuitry underlying pluripotency. These studies have, as a consequence, uncovered fundamental mechanisms that control mammalian gene expression, connect gene expression to chromosome structure, and contribute to human disease. Embryonic stem cells (ESCs) are pluripotent, self-renewing cells that are derived from the inner cell mass (ICM) of the developing blastocyst. Pluripotency is the capacity of a single cell to generate all cell lineages of the developing and adult organism. Self-renewal is the ability of a cell to proliferate in the same state. The molecular mechanisms that control ESC pluripotency and self-renewal are important to discover because they are key to understanding development. Because defects in development cause many different diseases, improved understanding of control mechanisms in pluripotent cells may lead to new therapies for these diseases. ESCs have a gene expression program that allows them to self-renew yet remain poised to differentiate into essentially all cell types in response to developmental cues. Recent reviews have discussed ESCs and developmental potency (Rossant, 2008Rossant J. Stem cells and early lineage development.Cell. 2008; 132: 527-531Abstract Full Text Full Text PDF PubMed Scopus (153) Google Scholar), the nature of the pluripotent ground state of ESCs (Silva and Smith, 2008Silva J. Smith A. Capturing pluripotency.Cell. 2008; 132: 532-536Abstract Full Text Full Text PDF PubMed Scopus (196) Google Scholar), ESC transcriptional regulatory circuitry (Chen et al., 2008aChen X. Vega V.B. Ng H.H. Transcriptional regulatory networks in embryonic stem cells.Cold Spring Harb. Symp. Quant. Biol. 2008; 73: 203-209Crossref PubMed Scopus (28) Google Scholar, Jaenisch and Young, 2008Jaenisch R. Young R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming.Cell. 2008; 132: 567-582Abstract Full Text Full Text PDF PubMed Scopus (622) Google Scholar, Macarthur et al., 2009Macarthur B.D. Ma'ayan A. Lemischka I.R. Systems biology of stem cell fate and cellular reprogramming.Nat. Rev. Mol. Cell Biol. 2009; 10: 672-681PubMed Google Scholar, Orkin et al., 2008Orkin S.H. Wang J. Kim J. Chu J. Rao S. Theunissen T.W. Shen X. Levasseur D.N. The transcriptional network controlling pluripotency in ES cells.Cold Spring Harb. Symp. Quant. Biol. 2008; 73: 195-202Crossref PubMed Scopus (32) Google Scholar), the influence of extrinsic factors on pluripotency (Pera and Tam, 2010Pera M.F. Tam P.P. Extrinsic regulation of pluripotent stem cells.Nature. 2010; 465: 713-720Crossref PubMed Scopus (103) Google Scholar), and cellular reprogramming into ESC-like states (Hanna et al., 2010Hanna J.H. Saha K. Jaenisch R. Pluripotency and cellular reprogramming: Facts, hypotheses, unresolved issues.Cell. 2010; 143: 508-525Abstract Full Text Full Text PDF PubMed Scopus (245) Google Scholar, Stadtfeld and Hochedlinger, 2010Stadtfeld M. Hochedlinger K. Induced pluripotency: history, mechanisms, and applications.Genes Dev. 2010; 24: 2239-2263Crossref PubMed Scopus (250) Google Scholar, Yamanaka and Blau, 2010Yamanaka S. Blau H.M. Nuclear reprogramming to a pluripotent state by three approaches.Nature. 2010; 465: 704-712Crossref PubMed Scopus (272) Google Scholar). This Review provides a synthesis of key concepts that explain how pluripotency and self-renewal are controlled transcriptionally. These concepts have emerged from genetic, biochemical, and molecular studies of the transcription factors, cofactors, chromatin regulators, and noncoding RNAs (ncRNAs) that control the ESC gene expression program. The regulators of gene expression programs can participate in gene activation, establish a poised state for gene activation in response to developmental cues, or contribute to gene silencing (Figure 1). The molecular mechanisms by which these regulators generally participate in control of gene expression are the subject of other reviews (Bartel, 2009Bartel D.P. MicroRNAs: Target recognition and regulatory functions.Cell. 2009; 136: 215-233Abstract Full Text Full Text PDF PubMed Scopus (3595) Google Scholar, Bonasio et al., 2010Bonasio R. Tu S. Reinberg D. Molecular signals of epigenetic states.Science. 2010; 330: 612-616Crossref PubMed Scopus (221) Google Scholar, Fuda et al., 2009Fuda N.J. Ardehali M.B. Lis J.T. Defining mechanisms that regulate RNA polymerase II transcription in vivo.Nature. 2009; 461: 186-192Crossref PubMed Scopus (183) Google Scholar, Ho and Crabtree, 2010Ho L. Crabtree G.R. Chromatin remodelling during development.Nature. 2010; 463: 474-484Crossref PubMed Scopus (254) Google Scholar, Li et al., 2007Li B. Carey M. Workman J.L. The role of chromatin during transcription.Cell. 2007; 128: 707-719Abstract Full Text Full Text PDF PubMed Scopus (1385) Google Scholar, Roeder, 2005Roeder R.G. Transcriptional regulation and the role of diverse coactivators in animal cells.FEBS Lett. 2005; 579: 909-915Abstract Full Text Full Text PDF PubMed Scopus (184) Google Scholar, Surface et al., 2010Surface L.E. Thornton S.R. Boyer L.A. Polycomb group proteins set the stage for early lineage commitment.Cell Stem Cell. 2010; 7: 288-298Abstract Full Text Full Text PDF PubMed Scopus (89) Google Scholar, Taatjes, 2010Taatjes D.J. The human Mediator complex: a versatile, genome-wide regulator of transcription.Trends Biochem. Sci. 2010; 35: 315-322Abstract Full Text Full Text PDF PubMed Scopus (122) Google Scholar). I describe here the regulators that have been implicated in control of ESC state and discuss how they contribute to the gene expression program of pluripotency and self-renewal. ESCs are perhaps unique in that they've been the subject of virtually every scale of investigation from large-scale genomics and protein-DNA interaction studies to highly focused mechanistic studies of individual regulatory factors. The combined results of these systems-level and molecular approaches offer a definition of embryonic stem cell state in terms of global gene regulation, which serves as both a baseline for understanding the changes that occur as cells differentiate and develop and as a means to understand the basic biology of these cells. For the purposes of this Review, this “state” is the product of all the regulatory inputs that produce the gene expression program of pluripotent, self-renewing cells. The most important regulatory inputs in ESCs appear to come from a small number of “core” transcription factors acting in concert with other transcription factors, some of which are terminal components of developmental signaling pathways. Transcription factors recognize specific DNA sequences and either activate or prevent transcription. Early studies into the transcriptional control of the E. coli lac operon created the framework for understanding gene control (Jacob and Monod, 1961Jacob F. Monod J. Genetic regulatory mechanisms in the synthesis of proteins.J. Mol. Biol. 1961; 3: 318-356Crossref PubMed Google Scholar). In the absence of lactose, the lac operon is repressed by the Lac repressor, which binds the lac operator and inhibits transcription by RNA polymerase. In the presence of lactose, the Lac repressor is lost and gene expression is activated by a transcription-activating factor that binds a nearby site and recruits RNA polymerase. The fundamental concept that emerged from these studies—that gene control relies on specific repressors and activators and the DNA sequence elements they recognize—continues to provide the foundation for understanding control of gene expression in all organisms. In mammals, transcription factors make up the largest single class of proteins encoded in the genome, representing approximately 10% of all protein-coding genes (Levine and Tjian, 2003Levine M. Tjian R. Transcription regulation and animal diversity.Nature. 2003; 424: 147-151Crossref PubMed Scopus (625) Google Scholar, Vaquerizas et al., 2009Vaquerizas J.M. Kummerfeld S.K. Teichmann S.A. Luscombe N.M. A census of human transcription factors: function, expression and evolution.Nat. Rev. Genet. 2009; 10: 252-263Crossref PubMed Scopus (250) Google Scholar). Transcription factors bind both to promoter-proximal DNA elements and to more distal regions that can be nearby or 100s of kb away. The elements that are involved in positive gene regulation are called enhancers, and these elements are generally bound by multiple transcription factors. Transcription factors can activate gene expression by recruiting the transcription apparatus and/or by stimulating release of RNA polymerase II from pause sites (Fuda et al., 2009Fuda N.J. Ardehali M.B. Lis J.T. Defining mechanisms that regulate RNA polymerase II transcription in vivo.Nature. 2009; 461: 186-192Crossref PubMed Scopus (183) Google Scholar). They can also recruit various chromatin regulators to promoter regions to modify and mobilize nucleosomes in order to increase access to local DNA sequences (Li et al., 2007Li B. Carey M. Workman J.L. The role of chromatin during transcription.Cell. 2007; 128: 707-719Abstract Full Text Full Text PDF PubMed Scopus (1385) Google Scholar). In ESCs, the pluripotent state is largely governed by the core transcription factors Oct4, Sox2, and Nanog (Table 1) (Chambers and Smith, 2004Chambers I. Smith A. Self-renewal of teratocarcinoma and embryonic stem cells.Oncogene. 2004; 23: 7150-7160Crossref PubMed Scopus (317) Google Scholar, Niwa, 2007Niwa H. How is pluripotency determined and maintained?.Development. 2007; 134: 635-646Crossref PubMed Scopus (380) Google Scholar, Silva and Smith, 2008Silva J. Smith A. Capturing pluripotency.Cell. 2008; 132: 532-536Abstract Full Text Full Text PDF PubMed Scopus (196) Google Scholar). Oct4 and Nanog were identified as key regulators based on their relatively unique expression pattern in ESCs and genetic experiments showing that they are essential for establishing or maintaining a robust pluripotent state (Chambers et al., 2003Chambers I. Colby D. Robertson M. Nichols J. Lee S. Tweedie S. Smith A. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells.Cell. 2003; 113: 643-655Abstract Full Text Full Text PDF PubMed Scopus (1674) Google Scholar, Chambers and Smith, 2004Chambers I. Smith A. Self-renewal of teratocarcinoma and embryonic stem cells.Oncogene. 2004; 23: 7150-7160Crossref PubMed Scopus (317) Google Scholar, Mitsui et al., 2003Mitsui K. Tokuzawa Y. Itoh H. Segawa K. Murakami M. Takahashi K. Maruyama M. Maeda M. Yamanaka S. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells.Cell. 2003; 113: 631-642Abstract Full Text Full Text PDF PubMed Scopus (1582) Google Scholar, Nichols et al., 1998Nichols J. Zevnik B. Anastassiadis K. Niwa H. Klewe-Nebenius D. Chambers I. Scholer H. Smith A. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4.Cell. 1998; 95: 379-391Abstract Full Text Full Text PDF PubMed Scopus (1672) Google Scholar, Niwa et al., 2000Niwa H. Miyazaki J. Smith A.G. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells.Nat. Genet. 2000; 24: 372-376Crossref PubMed Scopus (1865) Google Scholar). Oct4 functions as a heterodimer with Sox2 in ESCs, thus placing Sox2 among the key regulators (Ambrosetti et al., 2000Ambrosetti D.C. Scholer H.R. Dailey L. Basilico C. 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. 2000; 275: 23387-23397Crossref PubMed Scopus (99) Google Scholar, Avilion et al., 2003Avilion A.A. Nicolis S.K. Pevny L.H. Perez L. Vivian N. Lovell-Badge R. Multipotent cell lineages in early mouse development depend on SOX2 function.Genes Dev. 2003; 17: 126-140Crossref PubMed Scopus (1015) Google Scholar, Masui et al., 2007Masui S. Nakatake Y. Toyooka Y. Shimosato D. Yagi R. Takahashi K. Okochi H. Okuda A. Matoba R. Sharov A.A. et al.Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells.Nat. Cell Biol. 2007; 9: 625-635Crossref PubMed Scopus (412) Google Scholar). Reprogramming of somatic cells into induced pluripotent stem (iPS) cells generally requires forced expression of Oct4 and Sox2, unless endogenous Sox2 is expressed in the somatic cell, consistent with the view that Oct4/Sox2 are key to establishing the ESC state (Hanna et al., 2010Hanna J.H. Saha K. Jaenisch R. Pluripotency and cellular reprogramming: Facts, hypotheses, unresolved issues.Cell. 2010; 143: 508-525Abstract Full Text Full Text PDF PubMed Scopus (245) Google Scholar, Stadtfeld and Hochedlinger, 2010Stadtfeld M. Hochedlinger K. Induced pluripotency: history, mechanisms, and applications.Genes Dev. 2010; 24: 2239-2263Crossref PubMed Scopus (250) Google Scholar, Yamanaka and Blau, 2010Yamanaka S. Blau H.M. Nuclear reprogramming to a pluripotent state by three approaches.Nature. 2010; 465: 704-712Crossref PubMed Scopus (272) Google Scholar). Although ESCs can be propagated in the absence of Nanog (Chambers et al., 2007Chambers I. Silva J. Colby D. Nichols J. Nijmeijer B. Robertson M. Vrana J. Jones K. Grotewold L. Smith A. Nanog safeguards pluripotency and mediates germline development.Nature. 2007; 450: 1230-1234Crossref PubMed Scopus (543) Google Scholar), Nanog promotes a stable undifferentiated ESC state (Chambers et al., 2007Chambers I. Silva J. Colby D. Nichols J. Nijmeijer B. Robertson M. Vrana J. Jones K. Grotewold L. Smith A. Nanog safeguards pluripotency and mediates germline development.Nature. 2007; 450: 1230-1234Crossref PubMed Scopus (543) Google Scholar), is necessary for pluripotency to develop in ICM cells (Silva et al., 2009Silva J. Nichols J. Theunissen T.W. Guo G. van Oosten A.L. Barrandon O. Wray J. Yamanaka S. Chambers I. Smith A. Nanog is the gateway to the pluripotent ground state.Cell. 2009; 138: 722-737Abstract Full Text Full Text PDF PubMed Scopus (320) Google Scholar), and co-occupies most sites with Oct4 and Sox2 throughout the ESC genome (Marson et al., 2008bMarson A. Levine S.S. Cole M.F. Frampton G.M. Brambrink T. Johnstone S. Guenther M.G. Johnston W.K. Wernig M. Newman J. et al.Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells.Cell. 2008; 134: 521-533Abstract Full Text Full Text PDF PubMed Scopus (628) Google Scholar), so it is included here as a component of the core regulatory circuitry.Table 1Transcriptional Regulators Implicated in Control of ESC StateType of RegulatorFunctionReferencesTranscription FactorsOct4Core circuitry1Sox2Core circuitry2NanogCore circuitry3Tcf3Wnt signaling to core circuitry4Stat3Lif signaling to core circuitry5Smad1BMP signaling to core circuitry6Smad2/3TGF-β/Activin/Nodal signaling7c-MycProliferation8EsrrbSteroid hormone receptor9Sall4Embryonic regulator10Tbx3Mediates LIF signaling11ZfxSelf-renewal12RoninMetabolism13Klf4LIF signaling14Prdm14ESC identity15CofactorsMediatorCore circuitry16CohesinCore circuitry17Paf1 complexCouples transcription with histone modification18Dax1Oct4 inhibitor19Cnot3Myc/Zfx cofactor20Trim28Myc/Zfx cofactor21Chromatin RegulatorsPolycomb groupSilencing of lineage-specific regulators22SetDB1 (ESET)Silencing of lineage-specific regulators23esBAFNucleosome mobilization24Chd1Nucleosome mobilization25Chd7Nucleosome mobilization26Tip60-p400Histone acetylation27ncRNA RegulatorsmiRNAsFine-tuning of pluripotency transcripts28GC-rich ncRNAsPcG complex recruitment29The vast majority of these regulators were identified in murine ES cells, but most appear to play similar roles in human ES cells. LIF-Stat3 signaling is important for maintenance of murine ESCs and Activin-Smad2/3 signaling has been demonstrated to be important for human ESCs.References: 1 (Chambers et al., 2003Chambers I. Colby D. Robertson M. Nichols J. Lee S. Tweedie S. Smith A. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells.Cell. 2003; 113: 643-655Abstract Full Text Full Text PDF PubMed Scopus (1674) Google Scholar, Chambers and Smith, 2004Chambers I. Smith A. Self-renewal of teratocarcinoma and embryonic stem cells.Oncogene. 2004; 23: 7150-7160Crossref PubMed Scopus (317) Google Scholar, Hart et al., 2004Hart A.H. Hartley L. Ibrahim M. Robb L. Identification, cloning and expression analysis of the pluripotency promoting Nanog genes in mouse and human.Dev. Dyn. 2004; 230: 187-198Crossref PubMed Scopus (172) Google Scholar, Mitsui et al., 2003Mitsui K. Tokuzawa Y. Itoh H. Segawa K. Murakami M. Takahashi K. Maruyama M. Maeda M. Yamanaka S. 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• W2017050785 created "2016-06-24" @default.
• W2017050785 creator A5057814473 @default.
• W2017050785 date "2011-03-01" @default.
• W2017050785 modified "2023-10-13" @default.
• W2017050785 title "Control of the Embryonic Stem Cell State" @default.
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