SEARCH

SEARCH BY CITATION

References

  • Bailly A, Torres-Padilla ME, Tinel AP, Weiss MC (2001) An enhancer element 6 kb upstream of the mouse HNF4alpha1 promoter is activated by glucocorticoids and liver-enriched transcription factors. Nucleic Acids Res 29: 34953505
  • Bateman E (1998) Auto-regulation of eukaryotic transcription factors. Prog Nucleic Acid Res Mol Biol 60: 133168
  • Becskei A, Serrano L (2000) Engineering stability in gene networks by auto-regulation. Nature 405: 590593
  • Bell GI, Polonsky KS (2001) Diabetes mellitus and genetically programmed defects in beta-cell function. Nature 414: 788791
  • Blais A, Tsikitis M, Acosta-Alvear D, Sharan R, Kluger Y, Dynlacht BD (2005) An initial blueprint for myogenic differentiation. Genes Dev 19: 553569
  • Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122: 947956
  • Brandman O, Ferrell JE, Li R, Meyer T (2005) Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 310: 496498
  • Briancon N, Bailly A, Clotman F, Jacquemin P, Lemaigre FP, Weiss MC (2004) Expression of the alpha7 isoform of hepatocyte nuclear factor (HNF) 4 is activated by HNF6/OC-2 and HNF1 and repressed by HNF4alpha1 in the liver. J Biol Chem 279: 3339833408
  • Cereghini S (1996) Liver-enriched transcription factors and hepatocyte differentiation. FASEB J 10: 267282
  • Chen H, Ray-Gallet D, Zhang P, Hetherington CJ, Gonzalez DA, Zhang DE, Moreau-Gachelin F, Tenen DG (1995) PU.1 (Spi-1) auto-regulates its expression in myeloid cells. Oncogene 11: 15491560
  • Costa RH, Kalinichenko VV, Holterman AX, Wang X (2003) Transcription factors in liver development, differentiation, and regeneration. Hepatology 38: 13311347
  • Duncan SA, Navas MA, Dufort D, Rossant J, Stoffel M (1998) Regulation of a transcription factor network required for differentiation and metabolism. Science 281: 692695
  • Friedman JR, Larris B, Le PP, Peiris TH, Arsenlis A, Schug J, Tobias JW, Kaestner KH, Greenbaum LE (2004) Orthogonal analysis of C/EBPbeta targets in vivo during liver proliferation. Proc Natl Acad Sci USA 101: 1298612991
  • Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99104
  • Krivan W, Wasserman WW (2001) A predictive model for regulatory sequences directing liver-specific transcription. Genome Res 11: 15591566
  • Kuo CJ, Conley PB, Chen L, Sladek FM, Darnell Jr JE, Crabtree GR (1992) A transcriptional hierarchy involved in mammalian cell-type specification. Nature 355: 457461
  • Lee CS, Friedman JR, Fulmer JT, Kaestner KH (2005) The initiation of liver development is dependent on Foxa transcription factors. Nature 435: 944947
  • Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799804
  • Macisaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, Young RA, Fraenkel E (2006) A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics 22: 423429
  • Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002) Network motifs: simple building blocks of complex networks. Science 298: 824827
  • Montminy M, Koo SH, Zhang X (2004) The CREB family: key regulators of hepatic metabolism. Ann Endocrinol (Paris) 65: 7375
  • Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA (2004) Control of pancreas and liver gene expression by HNF transcription factors. Science 303: 13781381
  • Okumura-Nakanishi S, Saito M, Niwa H, Ishikawa F (2005) Oct-3/4 and Sox2 regulate Oct-3/4 gene in embryonic stem cells. J Biol Chem 280: 53075317
  • Pajukanta P, Lilja HE, Sinsheimer JS, Cantor RM, Lusis AJ, Gentile M, Duan XJ, Soro-Paavonen A, Naukkarinen J, Saarela J, Laakso M, Ehnholm C, Taskinen MR, Peltonen L (2004) Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1). Nat Genet 36: 371376
  • Pani L, Quian XB, Clevidence D, Costa RH (1992) The restricted promoter activity of the liver transcription factor hepatocyte nuclear factor 3 beta involves a cell-specific factor and positive autoactivation. Mol Cell Biol 12: 552562
  • Phuc Le P, Friedman JR, Schug J, Brestelli JE, Parker JB, Bochkis IM, Kaestner KH (2005) Glucocorticoid receptor-dependent gene regulatory networks. PLoS Genet 1: e16
  • Rada-Iglesias A, Wallerman O, Koch C, Ameur A, Enroth S, Clelland G, Wester K, Wilcox S, Dovey OM, Ellis PD, Wraight VL, James K, Andrews R, Langford C, Dhami P, Carter N, Vetrie D, Ponten F, Komorowski J, Dunham I, Wadelius C (2005) Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays. Hum Mol Genet 14: 34353447
  • Rosenfeld N, Elowitz MB, Alon U (2002) Negative auto-regulation speeds the response times of transcription networks. J Mol Biol 323: 785793
  • Rubins NE, Friedman JR, Le PP, Zhang L, Brestelli J, Kaestner KH (2005) Transcriptional networks in the liver: hepatocyte nuclear factor 6 function is largely independent of Foxa2. Mol Cell Biol 25: 70697077
  • Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 6468
  • Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101: 60626067
  • Tapscott SJ, Weintraub H (1991) MyoD and the regulation of myogenesis by helix–loop–helix proteins. J Clin Invest 87: 11331138
  • Thieffry D, Huerta AM, Perez-Rueda E, Collado-Vides J (1998) From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays 20: 433440
  • Tronche F, Ringeisen F, Blumenfeld M, Yaniv M, Pontoglio M (1997) Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J Mol Biol 266: 231245
  • Zaret KS (2002) Regulatory phases of early liver development: paradigms of organogenesis. Nat Rev Genet 3: 499512
  • Zeitlinger J, Simon I, Harbison CT, Hannett NM, Volkert TL, Fink GR, Young RA (2003) Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 113: 395404
  • Zhang X, Odom DT, Koo SH, Conkright MD, Canettieri G, Best J, Chen H, Jenner R, Herbolsheimer E, Jacobsen E, Kadam S, Ecker JR, Emerson B, Hogenesch JB, Unterman T, Young RA, Montminy M (2005) Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci USA 102: 44594464