An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

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

Bailey, 2006, MEME: discovering and analyzing DNA and protein sequence motifs, Nucleic. Acids Res., 34, 369, 10.1093/nar/gkl198

Bernstein, 2006, A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell, 125, 315, 10.1016/j.cell.2006.02.041

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

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

Cowan, 2005, Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells, Science, 309, 1369, 10.1126/science.1116447

de Boer, 2003, Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice, Proc. Natl. Acad. Sci. USA, 100, 7480, 10.1073/pnas.1332608100

Ernst, 1996, Gp130-mediated signal transduction in embryonic stem cells involves activation of Jak and Ras/mitogen-activated protein kinase pathways, J. Biol. Chem., 271, 30136, 10.1074/jbc.271.47.30136

Euskirchen, 2007, Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies, Genome Res., 17, 898, 10.1101/gr.5583007

Evans, 1981, Establishment in culture of pluripotential cells from mouse embryos, Nature, 292, 154, 10.1038/292154a0

Fernandez, 2003, Genomic targets of the human c-Myc protein, Genes Dev., 17, 1115, 10.1101/gad.1067003

Guccione, 2006, Myc-binding-site recognition in the human genome is determined by chromatin context, Nat. Cell Biol., 8, 764, 10.1038/ncb1434

Guenther, 2007, A chromatin landmark and transcription initiation at most promoters in human cells, Cell, 130, 77, 10.1016/j.cell.2007.05.042

Ivanova, 2006, Dissecting self-renewal in stem cells with RNA interference, Nature, 442, 533, 10.1038/nature04915

Iyer, 2001, Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF, Nature, 409, 533, 10.1038/35054095

Jeong, 2001, Lethality and centrality in protein networks, Nature, 411, 41, 10.1038/35075138

Johnson, 2006, Model-based analysis of tiling-arrays for ChIP-chip, Proc. Natl. Acad. Sci. USA, 103, 12457, 10.1073/pnas.0601180103

Kim, 2005, Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment, Nat. Methods, 2, 47, 10.1038/nmeth726

Kuhn, 2007, The UCSC genome browser database: update 2007, Nucleic Acids Res., 35, 668, 10.1093/nar/gkl928

Lee, 2006, Control of developmental regulators by Polycomb in human embryonic stem cells, Cell, 125, 301, 10.1016/j.cell.2006.02.043

Li, 2003, A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells, Proc. Natl. Acad. Sci. USA, 100, 8164, 10.1073/pnas.1332764100

Loh, 2006, The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells, Nat. Genet., 38, 431, 10.1038/ng1760

Macisaac, 2006, A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data, Bioinformatics, 22, 423, 10.1093/bioinformatics/bti815

Maherali, 2007, Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution, Cell Stem Cell, 1, 55, 10.1016/j.stem.2007.05.014

Mao, 2003, Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression, Curr. Biol., 13, 882, 10.1016/S0960-9822(03)00297-5

Martin, 1981, Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells, Proc. Natl. Acad. Sci. USA, 78, 7634, 10.1073/pnas.78.12.7634

Messina, 2004, An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression, Genome Res., 14, 2041, 10.1101/gr.2584104

Mi, 2007, PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways, Nucleic Acids Res., 35, D247, 10.1093/nar/gkl869

Mito, 2005, Genome-scale profiling of histone H3.3 replacement patterns, Nat. Genet., 37, 1090, 10.1038/ng1637

Mito, 2007, Histone replacement marks the boundaries of cis-regulatory domains, Science, 315, 1408, 10.1126/science.1134004

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

Nakagawa, 2007, Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts, Nat. Biotechnol., 26, 101, 10.1038/nbt1374

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

Okita, 2007, Generation of germline-competent induced pluripotent stem cells, Nature, 448, 313, 10.1038/nature05934

Orkin, 2005, Chipping away at the embryonic stem cell network, Cell, 122, 828, 10.1016/j.cell.2005.09.002

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

Park, 2007, Reprogramming of human somatic cells to pluripotency with defined factors, Nature, 451, 141, 10.1038/nature06534

Pirity, 2005, Rybp/DEDAF is required for early postimplantation and for central nervous system development, Mol. Cell. Biol., 25, 7193, 10.1128/MCB.25.16.7193-7202.2005

Ren, 2000, Genome-wide location and function of DNA binding proteins, Science, 290, 2306, 10.1126/science.290.5500.2306

Roh, 2004, High-resolution genome-wide mapping of histone modifications, Nat. Biotechnol., 22, 1013, 10.1038/nbt990

Sakaki-Yumoto, 2006, The murine homolog of SALL4, a causative gene in Okihiro syndrome, is essential for embryonic stem cell proliferation, and cooperates with Sall1 in anorectal, heart, brain and kidney development, Development, 133, 3005, 10.1242/dev.02457

Silva, 2006, Nanog promotes transfer of pluripotency after cell fusion, Nature, 441, 997, 10.1038/nature04914

Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. USA, 102, 15545, 10.1073/pnas.0506580102

Takahashi, 2007, Induction of pluripotent stem cells from adult human fibroblasts by defined factors, Cell, 131, 861, 10.1016/j.cell.2007.11.019

Takahashi, 2006, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 126, 663, 10.1016/j.cell.2006.07.024

Walhout, 2006, Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping, Genome Res., 16, 1445, 10.1101/gr.5321506

Wang, 2006, A protein interaction network for pluripotency of embryonic stem cells, Nature, 444, 364, 10.1038/nature05284

Wernig, 2007, C-Myc is dispensable for direct reprogramming of mouse fibroblasts, Cell Stem Cell, 2, 10, 10.1016/j.stem.2007.12.001

Wernig, 2007, In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state, Nature, 448, 318, 10.1038/nature05944

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

Yoshida, 1994, Maintenance of the pluripotential phenotype of embryonic stem cells through direct activation of gp130 signalling pathways, Mech. Dev., 45, 163, 10.1016/0925-4773(94)90030-2

Yu, 2007, Induced pluripotent stem cell lines derived from human somatic cells, Science, 318, 1917, 10.1126/science.1151526

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

Zhao, 2007, Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells, Cell Stem Cell, 1, 286, 10.1016/j.stem.2007.08.004

Zhou, 2007, A gene regulatory network in mouse embryonic stem cells, Proc. Natl. Acad. Sci. USA, 104, 16438, 10.1073/pnas.0701014104