Genome-wide computational analysis of dioxin response element location and distribution in the human, mouse, and rat genomes

Chemical Research in Toxicology

Volumn 24, Issue 4, 2011, Pages 494-504

  Dere, Edward ^a   Forgacs, Agnes L ^a,b   Zacharewski, Timothy R ^a,b   Burgoon, Lyle D ^a,b  

^a Michigan State University   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2,3,7,8 TETRACHLORODIBENZO PARA DIOXIN; AROMATIC HYDROCARBON RECEPTOR;

ARTICLE; CHROMOSOME ANALYSIS; DIOXIN RESPONSE ELEMENT; GENE; GENE MAPPING; GENE SEQUENCE; GENOME ANALYSIS; HUMAN; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROMOTER REGION; RAT; SIGNAL TRANSDUCTION; X CHROMOSOME; Y CHROMOSOME;

ANIMALS; BASE SEQUENCE; CHROMOSOMES; CYTOCHROME P-450 CYP1A1; GENOME; GENOME, HUMAN; GENOMICS; HUMANS; LIGANDS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; RATS; RECEPTORS, ARYL HYDROCARBON; RESPONSE ELEMENTS; TETRACHLORODIBENZODIOXIN; TRANSCRIPTION INITIATION SITE;

RATTUS;

EID: 79954496051     PISSN: 0893228X     EISSN: 15205010     Source Type: Journal    
DOI: 10.1021/tx100328r     Document Type: Article

References (61)

1. Carroll, J. S., Liu, X. S., Brodsky, A. S., Li, W., Meyer, C. A., Szary, A. J., Eeckhoute, J., Shao, W., Hestermann, E. V., Geistlinger, T. R., Fox, E. A., Silver, P. A., and Brown, M. (2005) Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1 Cell 122, 33-43 (Pubitemid 40977938)
2. Carroll, J. S., Meyer, C. A., Song, J., Li, W., Geistlinger, T. R., Eeckhoute, J., Brodsky, A. S., Keeton, E. K., Fertuck, K. C., Hall, G. F., Wang, Q., Bekiranov, S., Sementchenko, V., Fox, E. A., Silver, P. A., Gingeras, T. R., Liu, X. S., and Brown, M. (2006) Genome-wide analysis of estrogen receptor binding sites Nat. Genet. 38, 1289-1297 (Pubitemid 44646291)
3. Lin, C.-Y., Vega, V. B., Thomsen, J. S., Zhang, T., Kong, S. L., Xie, M., Chiu, K. P., Lipovich, L., Barnett, D. H., Stossi, F., Yeo, A., George, J., Kuznetsov, V. A., Lee, Y. K., Charn, T. H., Palanisamy, N., Miller, L. D., Cheung, E., Katzenellenbogen, B. S., Ruan, Y., Bourque, G., Wei, C.-L., and Liu, E. T. (2007) Whole-genome cartography of estrogen receptor alpha binding sites PLoS Genet. 3, e87
4. Wederell, E. D., Bilenky, M., Cullum, R., Thiessen, N., Dagpinar, M., Delaney, A., Varhol, R., Zhao, Y., Zeng, T., Bernier, B., Ingham, M., Hirst, M., Robertson, G., Marra, M. A., Jones, S., and Hoodless, P. A. (2008) Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing Nucleic Acids Res. 36, 4549-4564
5. Gu, Y., Hogenesch, J., and Bradfield, C. (2000) The PAS superfamily: Sensors of environmental and developmental signals Annu. Rev. Pharmacol. Toxicol. 40, 519-561 (Pubitemid 30340692)
6. Denison, M. S. and Heath-Pagliuso, S. (1998) The Ah receptor: A regulator of the biochemical and toxicological actions of structurally diverse chemicals Bull. Environ. Contam. Toxicol. 61, 557-568 (Pubitemid 29010859)
7. Poland, A. and Knutson, J. C. (1982) 2,3,7,8-tetrachlorodibenzo-p-dioxin and related halogenated aromatic hydrocarbons: Examination of the mechanism of toxicity Annu. Rev. Pharmacol. Toxicol. 22, 517-554
8. Hankinson, O. (1995) The aryl hydrocarbon receptor complex Annu. Rev. Pharmacol. Toxicol. 35, 307-340
9. Swanson, H., Chan, W., and Bradfield, C. (1995) DNA binding specificities and pairing rules of the Ah receptor, ARNT, and SIM proteins J. Biol. Chem. 270, 26292-26302
10. Gillesby, B. E., Stanostefano, M., Porter, W., Safe, S., Wu, Z. F., and Zacharewski, T. R. (1997) Identification of a motif within the 5′ regulatory region of pS2 which is responsible for AP-1 binding and TCDD-mediated suppression Biochemistry 36, 6080-6089 (Pubitemid 27257874)
11. Lusska, A., Shen, E., and Whitlock, J. P. (1993) Protein-DNA interactions at a dioxin-responsive enhancer. Analysis of six bona fide DNA-binding sites for the liganded Ah receptor J. Biol. Chem. 268, 6575-6580 (Pubitemid 23099359)
12. Shen, E. S. and Whitlock, J. P. (1992) Protein-DNA interactions at a dioxin-responsive enhancer. Mutational analysis of the DNA-binding site for the liganded Ah receptor J. Biol. Chem. 267, 6815-6819
13. Quandt, K., Frech, K., Karas, H., Wingender, E., and Werner, T. (1995) MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data Nucleic Acids Res. 23, 4878-4884 (Pubitemid 3008389)
14. Sun, Y. V., Boverhof, D. R., Burgoon, L. D., Fielden, M. R., and Zacharewski, T. R. (2004) Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences Nucleic Acids Res. 32, 4512-4523 (Pubitemid 39317729)
15. Church, D. M., Goodstadt, L., Hillier, L. W., Zody, M. C., Goldstein, S., She, X., Bult, C. J., Agarwala, R., Cherry, J. L., DiCuccio, M., Hlavina, W., Kapustin, Y., Meric, P., Maglott, D., Birtle, Z., Marques, A. C., Graves, T., Zhou, S., Teague, B., Potamousis, K., Churas, C., Place, M., Herschleb, J., Runnheim, R., Forrest, D., Amos-Landgraf, J., Schwartz, D. C., Cheng, Z., Lindblad-Toh, K., Eichler, E. E., Ponting, C. P., and Consortium, M. G. S. (2009) Lineage-specific biology revealed by a finished genome assembly of the mouse PLoS Biol. 7, e1000112
16. Worley, K. C., Weinstock, G. M., and Gibbs, R. A. (2008) Rats in the genomic era Physiol. Genomics 32, 273-282 (Pubitemid 351328551)
17. Zody, M. C., Jiang, Z., Fung, H.-C., Antonacci, F., Hillier, L. W., Cardone, M. F., Graves, T. A., Kidd, J. M., Cheng, Z., Abouelleil, A., Chen, L., Wallis, J., Glasscock, J., Wilson, R. K., Reily, A. D., Duckworth, J., Ventura, M., Hardy, J., Warren, W. C., and Eichler, E. E. (2008) Evolutionary toggling of the MAPT 17q21.31 inversion region Nat. Genet. 40, 1076-1083
18. Emi, Y., Ikushiro, S., and Iyanagi, T. (1996) Xenobiotic responsive element-mediated transcriptional activation in the UDP-glucuronosyltransferase family 1 gene complex J. Biol. Chem. 271, 3952-3958 (Pubitemid 26065720)
19. Favreau, L. and Pickett, C. (1991) Transcriptional regulation of the rat NAD(P)H:quinone reductase gene. Identification of regulatory elements controlling basal level expression and inducible expression by planar aromatic compounds and phenolic antioxidants J. Biol. Chem. 266, 4556-4561 (Pubitemid 21909392)
20. Fujisawa-Sehara, A., Sogawa, K., Yamane, M., and Fujii-Kuriyama, Y. (1987) Characterization of xenobiotic responsive elements upstream from the drug-metabolizing cytochrome P-450c gene: A similarity to glucocorticoid regulatory elements Nucleic Acids Res. 15, 4179-4191
21. Pimental, R. A., Liang, B., Yee, G. K., Wilhelmsson, A., Poellinger, L., and Paulson, K. E. (1993) Dioxin receptor and C/EBP regulate the function of the glutathione S-transferase Ya gene xenobiotic response element Mol. Cell. Biol. 13, 4365-4373 (Pubitemid 23187665)
22. Yoo, H. Y., Chang, M. S., and Rho, H. M. (1999) Xenobiotic-responsive element for the transcriptional activation of the rat Cu/Zn superoxide dismutase gene Biochem. Biophys. Res. Commun. 256, 133-137 (Pubitemid 29298930)
23. Zhang, L., Savas, U., Alexander, D. L., and Jefcoate, C. R. (1998) Characterization of the mouse Cyp1B1 gene. Identification of an enhancer region that directs aryl hydrocarbon receptor-mediated constitutive and induced expression J. Biol. Chem. 273, 5174-5183 (Pubitemid 28108679)
24. Reisdorph, R. and Lindahl, R. (2007) Constitutive and 3-methylcholanthrene-induced rat ALDH3A1 expression is mediated by multiple xenobiotic response elements Drug Metab. Dispos. 35, 386-393 (Pubitemid 46333901)
25. Rhead, B., Karolchik, D., Kuhn, R., Hinrichs, A., Zweig, A., Fujita, P., Diekhans, M., Smith, K., Rosenbloom, K., Raney, B., Pohl, A., Pheasant, M., Meyer, L., Learned, K., Hsu, F., Hillman-Jackson, J., Harte, R., Giardine, B., Dreszer, T., Clawson, H., Barber, G., Haussler, D., and Kent, W. (2010) The UCSC Genome Browser database: update 2010 Nucleic Acids Res. 38, D613
26. Boverhof, D. R., Burgoon, L. D., Tashiro, C., Chittim, B., Harkema, J. R., Jump, D. B., and Zacharewski, T. R. (2005) Temporal and dose-dependent hepatic gene expression patterns in mice provide new insights into TCDD-Mediated hepatotoxicity Toxicol. Sci. 85, 1048-1063 (Pubitemid 40846879)
27. Eckel, J., Gennings, C., Therneau, T., Burgoon, L., Boverhof, D., and Zacharewski, T. (2005) Normalization of two-channel microarray experiments: A semiparametric approach Bioinformatics 21, 1078-1083 (Pubitemid 40467931)
28. Eckel, J., Gennings, C., Chinchilli, V., Burgoon, L., and Zacharewski, T. (2004) Empirical bayes gene screening tool for time-course or dose-response microarray data J. Biopharm. Stat. 14, 647-670 (Pubitemid 39296091)
29. Murray, I. A., Morales, J. L., Flaveny, C. A., Dinatale, B. C., Chiaro, C., Gowdahalli, K., Amin, S., and Perdew, G. H. (2010) Evidence for ligand-mediated selective modulation of aryl hydrocarbon receptor activity Mol. Pharmacol. 77, 247-254
30. Boutros, P. C., Yan, R., Moffat, I. D., Pohjanvirta, R., and Okey, A. B. (2008) Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: Comparison of rat and mouse BMC Genomics 9, 419
31. Boverhof, D. R., Burgoon, L. D., Tashiro, C., Sharratt, B., Chittim, B., Harkema, J. R., Mendrick, D. L., and Zacharewski, T. R. (2006) Comparative toxicogenomic analysis of the hepatotoxic effects of TCDD in Sprague Dawley rats and C57BL/6 mice Toxicol. Sci. 94, 398-416 (Pubitemid 44817156)
32. Fletcher, N., Wahlström, D., Lundberg, R., Nilsson, C. B., Nilsson, K. C., Stockling, K., Hellmold, H., and Håkansson, H. (2005) 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) alters the mRNA expression of critical genes associated with cholesterol metabolism, bile acid biosynthesis, and bile transport in rat liver: A microarray study Toxicol. Appl. Pharmacol. 207, 1-24 (Pubitemid 41073756)
33. Hayes, K., Zastrow, G., Nukaya, M., Pande, K., Glover, E., Maufort, J., Liss, A., Liu, Y., Moran, S., Vollrath, A., and Bradfield, C. (2007) Hepatic transcriptional networks induced by exposure to 2,3,7,8-tetrachlorodibenzo-p- dioxin Chem. Res. Toxicol. 20, 1573-1581 (Pubitemid 350275602)
34. Puga, A., Maier, A., and Medvedovic, M. (2000) The transcriptional signature of dioxin in human hepatoma HepG2 cells Biochem. Pharmacol. 60, 1129-1142
35. Tijet, N., Boutros, P. C., Moffat, I. D., Okey, A. B., Tuomisto, J., and Pohjanvirta, R. (2006) Aryl hydrocarbon receptor regulates distinct dioxin-dependent and dioxin-independent gene batteries Mol. Pharmacol. 69, 140-153 (Pubitemid 43048901)
36. Ovando, B. J., Vezina, C. M., McGarrigle, B. P., and Olson, J. R. (2006) Hepatic gene downregulation following acute and subchronic exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin Toxicol. Sci. 94, 428-438 (Pubitemid 44817158)
37. Yauk, C. L., Jackson, K., Malowany, M., and Williams, A. Lack of change in microRNA expression in adult mouse liver following treatment with benzo(a)pyrene despite robust mRNA transcriptional response. Mutat. Res. 2010, not supplied.
38. Bourdeau, V., Deschênes, J., Métivier, R., Nagai, Y., Nguyen, D., Bretschneider, N., Gannon, F., White, J. H., and Mader, S. (2004) Genome-wide identification of high-affinity estrogen response elements in human and mouse Mol. Endocrinol. 18, 1411-1427 (Pubitemid 38692179)
39. Lemay, D. G. and Hwang, D. H. (2006) Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics J. Lipid Res. 47, 1583-1587 (Pubitemid 44079913)
40. Menendez, D., Inga, A., and Resnick, M. A. (2010) Estrogen receptor acting in cis enhances WT and mutant p53 transactivation at canonical and noncanonical p53 target sequences Proc. Natl. Acad. Sci. U.S.A. 107, 1500-1505
41. Nukaya, M., Moran, S., and Bradfield, C. A. (2009) The role of the dioxin-responsive element cluster between the Cyp1a1 and Cyp1a2 loci in aryl hydrocarbon receptor biology Proc. Natl. Acad. Sci. U.S.A. 106, 4923-4928
42. Ortiz-Barahona, A., Villar, D., Pescador, N., Amigo, J., and Del Peso, L. (2010) Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription-profiling data and in silico binding site prediction Nucleic Acids Res. 38, 2332-2345
43. van Batenburg, M. F., Li, H., Polman, J. A., Lachize, S., Datson, N. A., Bussemaker, H. J., and Meijer, O. C. (2010) Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene PLoS ONE 5, e8839
44. Xue, Y., Sun, D., Daly, A., Yang, F., Zhou, X., Zhao, M., Huang, N., Zerjal, T., Lee, C., Carter, N. P., Hurles, M. E., and Tyler-Smith, C. (2008) Adaptive evolution of UGT2B17 copy-number variation Am. J. Hum. Genet. 83, 337-346
45. Farnham, P. J. (2009) Insights from genomic profiling of transcription factors Nat. Rev. Genet. 10, 605-616
46. Li, Q., Barkess, G., and Qian, H. (2006) Chromatin looping and the probability of transcription Trends Genet. 22, 197-202
47. Long, X. and Miano, J. M. (2007) Remote control of gene expression J. Biol. Chem. 282, 15941-15945 (Pubitemid 47100332)
48. Silkworth, J. B., Carlson, E. A., McCulloch, C., Illouz, K., Goodwin, S., and Sutter, T. R. (2008) Toxicogenomic analysis of gender, chemical, and dose effects in livers of TCDD- or aroclor 1254-exposed rats using a multifactor linear model Toxicol. Sci. 102, 291-309 (Pubitemid 351404900)
49. Walker, N. J., Wyde, M. E., Fischer, L. J., Nyska, A., and Bucher, J. R. (2006) Comparison of chronic toxicity and carcinogenicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in 2-year bioassays in female Sprague-Dawley rats Mol. Nutr. Food Res. 50, 934-944 (Pubitemid 44621798)
50. Twigger, S. N., Pruitt, K. D., Fernández-Suárez, X. M., Karolchik, D., Worley, K. C., Maglott, D. R., Brown, G., Weinstock, G., Gibbs, R. A., Kent, J., Birney, E., and Jacob, H. J. (2008) What everybody should know about the rat genome and its online resources Nat. Genet. 40, 523-527 (Pubitemid 351601234)
51. Saxonov, S., Berg, P., and Brutlag, D. L. (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters Proc. Natl. Acad. Sci. U.S.A. 103, 1412-1417 (Pubitemid 43191179)
52. Nakajima, M., Iwanari, M., and Yokoi, T. (2003) Effects of histone deacetylation and DNA methylation on the constitutive and TCDD-inducible expressions of the human CYP1 family in MCF-7 and HeLa cells Toxicol. Lett. 144, 247-256 (Pubitemid 36966733)
53. Badis, G., Berger, M. F., Philippakis, A. A., Talukder, S., Gehrke, A. R., Jaeger, S. A., Chan, E. T., Metzler, G., Vedenko, A., Chen, X., Kuznetsov, H., Wang, C.-F., Coburn, D., Newburger, D. E., Morris, Q., Hughes, T. R., and Bulyk, M. L. (2009) Diversity and complexity in DNA recognition by transcription factors Science 324, 1720-1723
54. Jaeger, S. A., Chan, E. T., Berger, M. F., Stottmann, R., Hughes, T. R., and Bulyk, M. L. (2010) Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites Genomics 95, 185-195
55. Cicatiello, L., Addeo, R., Sasso, A., Altucci, L., Petrizzi, V. B., Borgo, R., Cancemi, M., Caporali, S., Caristi, S., Scafoglio, C., Teti, D., Bresciani, F., Perillo, B., and Weisz, A. (2004) Estrogens and progesterone promote persistent CCND1 gene activation during G1 by inducing transcriptional derepression via c-Jun/c-Fos/estrogen receptor (progesterone receptor) complex assembly to a distal regulatory element and recruitment of cyclin D1 to its own gene promoter Mol. Cell. Biol. 24, 7260-7274 (Pubitemid 39014451)
56. Owen, G. I., Richer, J. K., Tung, L., Takimoto, G., and Horwitz, K. B. (1998) Progesterone regulates transcription of the p21(WAF1) cyclin- dependent kinase inhibitor gene through Sp1 and CBP/p300 J. Biol. Chem. 273, 10696-10701 (Pubitemid 28227684)
57. Stoecklin, E., Wissler, M., Schaetzle, D., Pfitzner, E., and Groner, B. (1999) Interactions in the transcriptional regulation exerted by Stat5 and by members of the steroid hormone receptor family J. Steroid Biochem. Mol. Biol. 69, 195-204 (Pubitemid 29305537)
58. Ahmed, S., Valen, E., Sandelin, A., and Matthews, J. (2009) Dioxin increases the interaction between aryl hydrocarbon receptor and estrogen receptor alpha at human promoters Toxicol. Sci. 111, 254-266
59. Beischlag, T. V. and Perdew, G. H. (2005) ER alpha-AHR-ARNT protein-protein interactions mediate estradiol-dependent transrepression of dioxin-inducible gene transcription J. Biol. Chem. 280, 21607-21611 (Pubitemid 40805729)
60. Boutros, P. C., Moffat, I. D., Franc, M. A., Tijet, N., Tuomisto, J., Pohjanvirta, R., and Okey, A. B. (2004) Dioxin-responsive AHRE-II gene battery: Identification by phylogenetic footprinting Biochem. Biophys. Res. Commun. 321, 707-715 (Pubitemid 39127408)
61. Sogawa, K., Numayama-Tsuruta, K., Takahashi, T., Matsushita, N., Miura, C., Nikawa, J.-i., Gotoh, O., Kikuchi, Y., and Fujii-Kuriyama, Y. (2004) A novel induction mechanism of the rat CYP1A2 gene mediated by Ah receptor-Arnt heterodimer Biochem. Biophys. Res. Commun. 318, 746-755 (Pubitemid 38624218)