Transcriptome profiling of human hepatocytes treated with Aroclor 1254 reveals transcription factor regulatory networks and clusters of regulated genes

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Reymann, Susanne ^a   Borlak, Jürgen ^a,b  

^a FRAUNHOFER INSTITUTE FOR TOXICOLOGY AND EXPERIMENTAL MEDICINE   (Germany)

^b HANNOVER MEDICAL SCHOOL   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AROCLOR 1254; AROMATIC HYDROCARBON RECEPTOR; COMPLEMENTARY DNA; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; EPIDERMAL GROWTH FACTOR; HOX PROTEIN; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ETS; WINGED HELIX TRANSCRIPTION FACTOR;

APOPTOSIS; ARTICLE; BINDING SITE; CELL CULTURE; CELL CYCLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LOCATION; GENE SEQUENCE; HUMAN; HUMAN CELL; HUMAN TISSUE; LIVER CELL; MOLECULAR RECOGNITION; NUCLEOTIDE SEQUENCE; PLEIOTROPY; PROMOTER REGION; PROTEIN BINDING; RNA ISOLATION; STATISTICAL SIGNIFICANCE; TRANSCRIPTION REGULATION; UNINDEXED SEQUENCE; WESTERN BLOTTING;

APOPTOSIS; BINDING SITES; CELL CYCLE; CELLS, CULTURED; CHLORODIPHENYL (54% CHLORINE); CHROMATIN; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN; GENE EXPRESSION REGULATION; HEPATOCYTES; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; TRANSCRIPTION FACTORS;

ANIMALIA;

EID: 33749375927     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-217     Document Type: Article

References (46)

1. Resendes KK, Rosmarin AG: SpI control of gene expression in myeloid cells. Crit Rev Eukaryot Gene Expr 2004, 14:171-81.
2. Mulder HJ, Saloheimo M, Penttila M, Madrid SM: The transcription factor HACA mediates the unfolded protein response in Aspergillus niger and up-regulates its own transcription. Mol Genet Genomics 2004, 271:130-40.
3. Mimur J, Fujii-Kuriyama Y: Functional role of AhR in the expression of toxic effects by TCDD. Biochim Biophys Acta 2003, 1619:263-8.
4. Whitlock JPJr, Chichester CH, Bedgood RM, Okino ST, Ko HP, Ma Q, Dong L, Li H, Clarke-Katzenberg R: Induction of drug-metabolizing enzymes by dioxin. Drug Metab Rey 1997, 29:1107-27.
5. Nebert DW, Roe AL, Dieter MZ Solis WA, Yang Y, Dalton TP: Role of the aromatic hydrocarbon receptor and [Ah] gene battery in the oxidative stress response cell cycle control and apoptosis. Biochem Pharmacol 2000, 59:65-85.
6. Niermann T, Schmutz S, Erne P, Resink T: Aryl hydrocarbon receptor ligands repress T-cadherin expression in vascular smooth muscle cells. Biochem Biophys Res Commun 2003, 300:943-9.
7. Dalton TP, Puga A, Shertzer HG: Induction of cellular oxidative stress by aryl hydrocarbon receptor activation. Chem Biol Interact 2002, 141:77-95.
8. Kolluri SK, Weiss C, Koff A, Gottlicher M: p27(Kipl) induction and inhibition of proliferation by the intracellular Ah receptor in developing thymus and hepatoma cells. Genes 1999, 13:1742-53.
9. Cohen BA, Mitra RD, Hughes JD, Church GM: A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 2000, 26:183-6.
10. Roy PJ, Stuart JM, Lund J, Kim SK: Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 2002, 418:975-9.
11. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI: Large clusters of co-expressed genes in the Drosophila genome. Nature 2002, 420:666-9.
12. Spellman PT, Rubin GM: Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 2002, 1:5. Epub 2002 Jun 18.
13. Lercher MJ, Urrutia AO, Hurst LD: Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 2002, 31:180-3.
14. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, Heisterkamp S, van Kampen A, Versteeg R: The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 2001, 291:1289-92.
15. Tong W, Harris S, Cao X, Fang H, Shi L, Sun H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins R, Casciano D: Development of public toxicogenomics software for microarray data management and analysis. Mutat Res 2004, 549(1-2):241-53.
16. NCBIs Gene Expression Omnibus (GEO) [http://www.ncbi.nlm.nih.gov/geo/]. See page 6.
17. Kel A, Reymann S, Matys V, Nettesheim P, Wingender E, Borlak J: A novel computational approach for the prediction of networked transcription factors of Ah-receptor regulated genes. Mol Pharmacol 2004, 66:1557-72. Epub 2004 Sep 01.
18. Wasserman WW, Fahl WE: Functional antioxidant responsive elements. Proc Natl Acad Sci USA 1997, 94:5361-6.
19. Jackson DA, Dickinson P, Cook PR: The size of chromatin loops in HeLa cells. EMBO J 1990, 9:567-571.
20. Safe S: Polychlorinated biphenyls (PCBs): environmental impact biochemical and toxic responses and implications for risk assessment. Crit Rev Toxicol 1994, 24:87-149.
21. Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe M, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M: Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci USA 2003, 100:12247-52.
22. Rayet B, Gelinas C: Aberrant rel/nfkb genes and activity in human cancer. Oncogene 1999, 18:6938-47.
23. Tian Y, Ke S, Denison MS, Rabson AB, Gallo MA: Ah receptor and NF-kappaB interactions a potential mechanism for dioxin toxicity. J Biol Chem 1999, 274:510-5.
24. Wang F, Wang W, Safe S: Regulation of constitutive gene expression through interactions of Spl protein with the nuclear aryl hydrocarbon receptor complex. Biochemistry 1999, 8:1490-500.
25. Yamada K, Tanaka T, Miyamoto K, Noguchi T: Sp Family Members and Nuclear Factor-Y Cooperatively Stimulate Transcription from the Rat Pyruvate Kinase M Gene Distal Promoter Region via Their Direct Interactions. J Biol Chem 2000, 215:18129-18137.
26. Puga A, Barnes SJ, Dalton TP, Chang C, Knudsen ES, Maier MA: Aromatic hydrocarbon receptor interaction with the retinoblastoma protein potentiates repression of E2F-dependent transcription and cell cycle arrest. J Biol Chem 2000, 275:2943-50.
27. Marlowe JL, Knudsen ES, Schwemberger S, Puga A: The aryl hydrocarbon receptor displaces p300 from E2F-dependent promoters and represses S phase-specific gene expression. J Biol Chem 2004, 279:29013-22. Epub 2004 Apr 30.
28. Chen BP, Liang G, Whelan J, Hai T: ATF3 and ATF3 delta Zip Transcriptional repression versus activation by alternatively spliced isoforms. J Biol Chem 1994, 269:15819-26.
29. Becuwe P, Dauça M: Comparison of cytotoxicity induced by hypolipidemic drugs via reactive oxygen species in human and rodent liver cells. Intern J Mol Med 2005, 16:483-492.
30. Wong ES, Fong CW, Lim J, Yusoff P, Low BC, Langdon WY, Guy GR: Sprouty2 attenuates epidermal growth factor receptor ubiquitylation and endocytosis and consequently enhances Ras/ERK signalling. EMBO J 2002, 21:4796-808.
31. Aguirre Ghiso JA, Alonso DF, Farias EF, Gomez DE, de Kier Joffe EB: Deregulation of the signaling pathways controlling urokinase production Its relationship with the invasive phenotype. Eur J Biochem 1999, 263:295-304.
32. Vaziri C, Faller DV: A benzo[a]pyrene-induced cell cycle checkpoint resulting in p53-independent GI arrest in 3T3 fibroblasts. J Biol Chem 1997, 272:2762-9.
33. Borlak J, Dangers M, Thum T: Aroclor 1254 modulates gene expression of nuclear transcription factors: implications for albumin gene transcription and protein synthesis in rat hepatocyte cultures. Toxicol Appl Pharmacol 2002, 81:79-88.
34. Borlak J, Hock A, Hansen T, Richter E: DNA adducts in cultures of polychlorinated biphenyl-treated human hepatocytes. Toxicol Appl Pharmacol 2003, 188:81-91.
35. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F: Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol 1999, 17:974-8.
36. Borlak JT, Scott A, Henderson CJ, Jenke HJ, Wolf CR: Transfer of PCBs via lactation simultaneously induces the expression of P450 isoenzymes and the protooncogenes c-Ha-ras and c-raf in neonates. Biochem Pharmacol 1996, 51:517-29.
37. NCBI database Entrez Gene [http://www.ncbi.nih.gov/entrez/ query.fcgi?db=gene.]. See page 22.
38. UCSC Genome Browser [http://genome.ucsc.edu/cgi-bin/hgGateway]. See page 22.
39. Quandt K, Frech K, Karas H, Wingender E, Werner T: MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res 1995, 23:4878-4884.
40. Whitlock JP: Induction of cytochrome P450IA. Annu Rev Pharmacol Toxicol 1999, 39:103-125.
41. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhäuser R, Prüé M, Schacherer F, Thiele S, Urbach S: The TRANSFAC system on gene expression regulation. Nucleic Acids Res 2001, 29:291-283.
42. BIOBASE Biological Databases [http://www.biobase.de/.]. See page 22.
43. Coleman SL, Buckland PR, Hoogendoorn B, Guy C, Smith K, O'Donovan MC: Experimental analysis of the annotation of promoters in the public database. Hum Mol Genet 2002, 11:1817-21.
44. Kel E, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E: MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 2003, 31:3576-3579.
45. GenomatixSoftwareGmbH [http://www.genomatix.de./.]. See page 23.
46. NCBI Genome Browser MapViewer [http://www.ncbi.nlm.nih.gov/mapview/.]. See page 23.