Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells

Cell - Tập 122 Số 6 - Trang 947-956 - 2005
Laurie A. Boyer1, Tong Ihn Lee1, Megan F. Cole2,1, Sarah E. Johnstone2,1, Stuart S. Levine1, Jacob Zucker3, Matthew G. Guenther1, Roshan Kumar1, Heather L. Murray1, Richard G. Jenner1, David K. Gifford4,5,1, Douglas A. Melton4,3, Rudolf Jaenisch2,1, Richard A. Young4,2,1
1Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142
2Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
3Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, 02138
4Broad Institute of MIT and Harvard, One Kendall Square, Building 300, Cambridge, Massachusetts 02139
5MIT Computer Science and Artificial Intelligence Laboratory (CSAIL), 32 Vassar Street, Cambridge, Massachusetts 02139

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Abeyta, 2004, Unique gene expression signatures of independently derived human embryonic stem cell lines, Hum. Mol. Genet., 13, 601, 10.1093/hmg/ddh068

Ambrosetti, 1997, Synergistic activation of the fibroblast growth factor 4 enhancer by Sox2 and Oct-3 depends on protein-protein interactions facilitated by a specific spatial arrangement of factor binding sites, Mol. Cell. Biol., 17, 6321, 10.1128/MCB.17.11.6321

Avilion, 2003, Multipotent cell lineages in early mouse development depend on SOX2 function, Genes Dev., 17, 126, 10.1101/gad.224503

Ballas, 2005, REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis, Cell, 121, 645, 10.1016/j.cell.2005.03.013

Bartel, 2004, MicroRNAs: genomics, biogenesis, mechanism, and function, Cell, 116, 281, 10.1016/S0092-8674(04)00045-5

Bortvin, 2003, Incomplete reactivation of Oct4-related genes in mouse embryos cloned from somatic nuclei, Development, 130, 1673, 10.1242/dev.00366

Botquin, 1998, New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2, Genes Dev., 12, 2073, 10.1101/gad.12.13.2073

Brandenberger, 2004, MPSS profiling of human embryonic stem cells, BMC Dev. Biol., 4, 10, 10.1186/1471-213X-4-10

Catena, 2004, Conserved POU binding DNA sites in the Sox2 upstream enhancer regulate gene expression in embryonic and neural stem cells, J. Biol. Chem., 279, 41846, 10.1074/jbc.M405514200

Chambers, 2004, The molecular basis of pluripotency in mouse embryonic stem cells, Cloning Stem Cells, 6, 386, 10.1089/clo.2004.6.386

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

Dailey, 2001, Coevolution of HMG domains and homeodomains and the generation of transcriptional regulation by Sox/POU complexes, J. Cell. Physiol., 186, 315, 10.1002/1097-4652(2001)9999:9999<000::AID-JCP1046>3.0.CO;2-Y

Guenther, 2005, Global and Hox-specific roles for the MLL1 methyltransferase, Proc. Natl. Acad. Sci. USA, 102, 8603, 10.1073/pnas.0503072102

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

Hay, 2004, Oct-4 knockdown induces similar patterns of endoderm and trophoblast differentiation markers in human and mouse embryonic stem cells, Stem Cells, 22, 225, 10.1634/stemcells.22-2-225

He, 2003, The transforming activity of Ski and SnoN is dependent on their ability to repress the activity of Smad proteins, J. Biol. Chem., 278, 30540, 10.1074/jbc.M304016200

Hombria, 2003, Beyond homeosis–HOX function in morphogenesis and organogenesis, Differentiation, 71, 461, 10.1046/j.1432-0436.2003.7108004.x

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

Kanellopoulou, 2005, Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing, Genes Dev., 19, 489, 10.1101/gad.1248505

Kuroda, 2005, Octamer and Sox elements are required for transcriptional cis regulation of Nanog gene expression, Mol. Cell. Biol., 25, 2475, 10.1128/MCB.25.6.2475-2485.2005

Lee, 2004, Histone deacetylase activity is required for embryonic stem cell differentiation, Genesis, 38, 32, 10.1002/gene.10250

Lee, 2002, Transcriptional regulatory networks in Saccharomyces cerevisiae, Science, 298, 799, 10.1126/science.1075090

Lewis, 2005, Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, 120, 15, 10.1016/j.cell.2004.12.035

Ma, 2004, An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs, Nucleic Acids Res., 32, 6643, 10.1093/nar/gkh1009

Mangan, 2003, Structure and function of the feed-forward loop network motif, Proc. Natl. Acad. Sci. USA, 100, 11980, 10.1073/pnas.2133841100

Mangan, 2003, The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks, J. Mol. Biol., 334, 197, 10.1016/j.jmb.2003.09.049

Matin, 2004, Specific knockdown of Oct4 and beta2-microglobulin expression by RNA interference in human embryonic stem cells and embryonic carcinoma cells, Stem Cells, 22, 659, 10.1634/stemcells.22-5-659

McAdams, 1997, Stochastic mechanisms in gene expression, Proc. Natl. Acad. Sci. USA, 94, 814, 10.1073/pnas.94.3.814

Milo, 2002, Network motifs: simple building blocks of complex networks, Science, 298, 824, 10.1126/science.298.5594.824

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

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

Nishimoto, 1999, The gene for the embryonic stem cell coactivator UTF1 carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2, Mol. Cell. Biol., 19, 5453, 10.1128/MCB.19.8.5453

Niwa, 2001, Molecular mechanism to maintain stem cell renewal of ES cells, Cell Struct. Funct., 26, 137, 10.1247/csf.26.137

Niwa, 2000, Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells, Nat. Genet., 24, 372, 10.1038/74199

Odom, 2004, Control of pancreas and liver gene expression by HNF transcription factors, Science, 303, 1378, 10.1126/science.1089769

Okumura-Nakanishi, 2005, Oct-3/4 and Sox2 regulate Oct-3/4 gene in embryonic stem cells, J. Biol. Chem., 280, 5307, 10.1074/jbc.M410015200

Pasquinelli, 2005, MicroRNAs: a developing story, Curr. Opin. Genet. Dev., 15, 200, 10.1016/j.gde.2005.01.002

Pera, 2004, Human embryonic stem cells: prospects for development, Development, 131, 5515, 10.1242/dev.01451

Pesce, 2001, Oct-4: gatekeeper in the beginnings of mammalian development, Stem Cells, 19, 271, 10.1634/stemcells.19-4-271

Remenyi, 2004, Combinatorial control of gene expression, Nat. Struct. Mol. Biol., 11, 812, 10.1038/nsmb820

Ren, 2002, E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints, Genes Dev., 16, 245, 10.1101/gad.949802

Resendis-Antonio, 2005, Modular analysis of the transcriptional regulatory network of E. coli, Trends Genet., 21, 16, 10.1016/j.tig.2004.11.010

Reubinoff, 2000, Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro, Nat. Biotechnol., 18, 399, 10.1038/74447

Rodda, D.J., Chew, J.-L., Lim, L.-H., Loh, Y.-H., Wang, B., Ng, H.-H., and Robson, P. (2005). Transcriptional regulation of Nanog by Oct4 and Sox2. J. Biol. Chem. 18, in press.

Rosenfeld, 2002, Negative autoregulation speeds the response times of transcription networks, J. Mol. Biol., 323, 785, 10.1016/S0022-2836(02)00994-4

Sato, 2003, Molecular signature of human embryonic stem cells and its comparison with the mouse, Dev. Biol., 260, 404, 10.1016/S0012-1606(03)00256-2

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

Schöler, 1990, Oct-4: a germline-specific transcription factor mapping to the mouse t-complex, EMBO J., 9, 2185, 10.1002/j.1460-2075.1990.tb07388.x

Shen-Orr, 2002, Network motifs in the transcriptional regulation network of Escherichia coli, Nat. Genet., 31, 64, 10.1038/ng881

Su, 2004, A gene atlas of the mouse and human protein-encoding transcriptomes, Proc. Natl. Acad. Sci. USA, 101, 6062, 10.1073/pnas.0400782101

Thieffry, 1998, Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12, Bioinformatics, 14, 391, 10.1093/bioinformatics/14.5.391

Thomson, 1998, Embryonic stem cell lines derived from human blastocysts, Science, 282, 1145, 10.1126/science.282.5391.1145

Wei, 2005, Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state, Stem Cells, 23, 166, 10.1634/stemcells.2004-0162

Weinmann, 2002, Isolating human transcription factor targets by coupling chromatin immunoprecipiation and CpG island microarray analysis, Genes Dev., 16, 235, 10.1101/gad.943102

Yuan, 1995, Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3, Genes Dev., 9, 2635, 10.1101/gad.9.21.2635

Zaehres, 2005, High-efficiency RNA interference in human embryonic stem cells, Stem Cells, 23, 299, 10.1634/stemcells.2004-0252