Transcriptomic analysis of Caenorhabditis elegans exposed to nickel (II) acetate using microarray

Biochip Journal

Volumn 5, Issue 1, 2011, Pages 78-85

  Jeong, Seok Won ^a,b   Seo, Young Rok ^a,b  

^a Dongguk University   (South Korea)

^b Kyung Hee University Hospital   (South Korea)

Author keywords

Biomarker; Caenorhabditis elegans; Comparative toxicogenomics database (CTD); Microarray; Nickel acetate

Indexed keywords

BIOMARKERS; BIOSENSORS; DATABASE SYSTEMS; DETOXIFICATION; GENES; NICKEL; NICKEL COMPOUNDS; ONTOLOGY; TOXICITY; VOLATILE FATTY ACIDS;

ANIMAL MODEL; CAENORHABDITIS ELEGANS; COMPARATIVE TOXICOGENOMICS DATABASE (CTD); ECO-TOXICOLOGY; ECOTOXICOLOGICAL; ELEGANS; GENE ONTOLOGY; GENETIC STUDIES; GENOMIC EXPRESSION; HISTONE MODIFICATION; HUMAN POPULATION; MOLECULAR COMPONENTS; MOLECULAR MECHANISM; NICKEL ACETATE; REPRODUCTIVE SYSTEMS; TOXICITY ASSESSMENT; TOXICOGENOMICS; WATER SOURCE;

ORGANOMETALLICS;

NICKEL; NICKEL(II) ACETATE; UNCLASSIFIED DRUG;

ARTICLE; CAENORHABDITIS ELEGANS; CARCINOGENESIS; COMPARATIVE TOXICOGENOMICS DATABASE; CONTROLLED STUDY; DETOXIFICATION; ECOTOXICOLOGY; ENVIRONMENTAL EXPOSURE; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC DATABASE; HAZARD ASSESSMENT; INFORMATION PROCESSING; MICROARRAY ANALYSIS; NONHUMAN; OXIDATIVE STRESS; TOXICOGENETICS; TRANSCRIPTOMICS;

ANIMALIA; CAENORHABDITIS ELEGANS;

EID: 79953058058     PISSN: 19760280     EISSN: 20927843     Source Type: Journal    
DOI: 10.1007/s13206-011-5112-5     Document Type: Article

References (36)

1. Kasprzak, K. S., Sunderman, F. W. Jr. & Salnikow, K. Nickel carcinogenesis. Mutat. Res. 533, 67-97 (2003).
2. Kodipura, D., Balakrishna, S., Thimappa, R. & Muralidhara. Nickel-induced oxidative stress in testis of mice: evidence of DNA damage and genotoxic effects. J. Androl. 25, 996-1003 (2004).
3. Wozniak, K. & Blasiak, J. Nickel impairs the repair of UV- and MNNG-damaged DNA. Cell Mol. Biol. Lett. 9, 83-94 (2004).
4. Harkin, A. et al. A toxicokinetic study of nickel-induced immunosuppression in rats. Immunopharmacol. Immunotoxicol. 25, 655-670 (2003).
5. Pandey, R., Kumar, R., Singh, S. P., Saxena, D. K. & Srivastava, S. P. Male reproductive effect of nickel sulphate in mice. Biometals12, 339-346 (1999).
6. Pandey, R. & Singh, S. P. Seminal toxicity of nickel sulfate in mice. Biol. Trace Elem. Res. 82, 211-215 (2001).
7. Ahn, J. I. et al. Changes of mi RNA and m RNA expression in HepG2 cells treated by epigallocatechin gallate. Mol. Cell. Toxicol. 6, 169-177 (2010).
8. Mattingly, C. J., Rosenstein, M. C., Colby, G. T., Forrest, J. N. Jr & Boyer, J. L. The comparative toxicogenomics database (CTD): a resource for comparative toxicological studies. J. Exp. Zool. A Comp. Exp. Biol. 305, 689-692 (2006).
9. Boyd, W. A., McBride, S. J. & Freedman, J. H. Effects of genetic mutations and chemical exposures on Caenorhabditis elegans feeding: evaluation of a novel, high-throughput screening assay. PLoS One12, e1259 (2007).
10. Consortium (The C. elegans sequencing consortium). Genome sequence of the nematode C. elegans: a platform for investigating biology. Science282, 2012-2018 (1998).
11. Reichert, K. & Menzel, R. Expression profiling of five different xenobiotics using a Caenorhabditis elegans whole genome microarray. Chemosphere61, 229-237 (2005).
12. Liao, V. H. C. & Freedman, J. H. Cadmium-regulated genes from Nematode Caenorhabditis elegans. J. Biol. Chem. 273, 31962-31970 (1998).
13. Yuxia, C. et al. Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity. Genome Biol. 8, R122 (2007).
14. Yang, Y. H. et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, 4e15 (2002).
15. Peng, X. et al. Statistical implications of pooling RNA samples for microarray experiments. BMC Bioinformatics4, 26 (2003).
16. Asikainen, S., Storvik, M., Lakso, M. & Wong, G. Whole genome microarray analysis of C. elegans rrf-3 and eri-1 mutants. FEBS Letters581, 5050-5054 (2007).
17. Rozen, S. & Skaletsky, H. Primer3 on the www for general users and for biologist programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (Krawetz, S. & Misener, S., eds.). Humana Press, Totowa, NJ. 365-386. (2000).
18. European Union. Technical guidance document on risk assessment in support of the commission directive 93/67/EEC on risk assessment for new notified substances Commission Regulation (EC) No 1488/94 on risk assessment for existing substances directive 98/8/ EC of the European Parliament and of the council concerning the placing of biocidal products on the market. 2nd version (2003).
19. Karaczyn, A. A., Golebiowski, F. & Kasprzak, K. S. Ni (II) affects ubiquitination of core histones H2B and H2A. Exp. Cell. Res. 312, 3252-3259 (2006).
20. Guengerich, F. P. Cytochrome P450 and chemical toxicology. Chem. Res. Toxicol. 21, 70-83 (2008).
21. Molina, A. R. D. et al. Choline kinase is a novel oncogene that potentiates RhoA-induced carcinogenesis. Cancer Res. 65, 5647-5653 (2005).
22. Nimmagadda, S., Glunde, K., Pomper, M. G. & Bhujwalla, J. M. Pharmacodynamic markers for choline kinase down-regulation in breast cancer cells. Neoplasia11, 477-484 (2009).
23. Hernandez-Alcoceba, R. et al. Choline kinase inhibitors as a novel approach for antiproliferative drug design. Oncogene15, 2289-2301 (1997).
24. Miller, A. F. Superoxide dismutases: active sites that save, but a protein that kills. Curr. Opin. Chem. Biol. 8, 162-168 (2004).
25. Keaney, M., Matthijssens, F., Sharpe, M., Vanfleteren, J. & Gems, D. Superoxide dismutase mimetics elevate superoxide dismutase activity in vivo but do not retard aging in the nematode Caenorhabditis elegans. Free Radic. Biol. Med. 37, 239-250 (2004).
26. Kawanishi, S., Oikawa, S., Inoue, S. & Nishino, K. Distinct mechanisms of oxidative DNA damage induced by carcinogenic nickel subsulfide and nickel oxides. Environ. Health Perspect. 110, 789-791 (2002).
27. Cavallo, D. et al. Evaluation of oxidative damage and inhibition of DNA repair in an in vitro study of nickel exposure. Toxicol. In Vitro17, 603-607 (2003).
28. Pourahmad, J., O'Brien, P. J., Jokar, F. & Daraei, B. Carcinogenic metal induced sites of reactive oxygen species formation in hepatocytes. Toxicol. In Vitro17, 803-810 (2003).
29. Gajewska, E. & Skłodowska, M. Effect of nickel on ROS content and antioxidative enzyme activities in wheat leaves. BioMetals20, 27-36 (2007).
30. Zhang, Y. Transcriptional regulation by histone ubiquitination and deubiquitination. Genes Dev. 17, 2733-2740 (2003).
31. Henry, K. W. et al. Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 17, 2648-2663 (2003).
32. Nathan, D., Sterner, D. E. & Berger, S. L. Histone modifications: now summoning sumoylation. Proc. Natl. Acad Sci. USA. 100, 13118-13120 (2003).
33. Shiio, Y. & Eisenman, R. N. Histone sumoylation is associated with transcriptional repression. Proc. Natl. Acad Sci. USA. 100, 13225-13230 (2003).
34. Hagiwara, T., Hidaka, Y. & Yamada, M. Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes. Biochemistry44, 5827-5834 (2005).
35. Kothapalli, N. et al. Biological functions of biotinylated histones, J. Nutr. Biochem. 16, 446-448 (2005).
36. Wood, A. et al. Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter, Mol. Cell11, 267-274 (2003).