Table of Contents
Advances in Toxicology
Volume 2014, Article ID 984319, 13 pages
http://dx.doi.org/10.1155/2014/984319
Research Article

Chemical Exposure Generates DNA Copy Number Variants and Impacts Gene Expression

1School of Health Sciences, Purdue University, 550 Stadium Mall Drive, HAMP-1263D, West Lafayette, IN 47907, USA
2Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA

Received 29 August 2014; Revised 3 December 2014; Accepted 3 December 2014; Published 30 December 2014

Academic Editor: Mugimane Manjanatha

Copyright © 2014 Samuel M. Peterson and Jennifer L. Freeman. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. The International HapMap Consortium, “A haplotype map of the human genome,” Nature, vol. 437, pp. 1299–1320, 2005. View at Publisher · View at Google Scholar
  2. A. J. Iafrate, L. Feuk, M. N. Rivera et al., “Detection of large-scale variation in the human genome,” Nature Genetics, vol. 36, no. 9, pp. 949–951, 2004. View at Publisher · View at Google Scholar · View at Scopus
  3. J. Sebat, B. Lakshmi, J. Troge et al., “Large-scale copy number polymorphism in the human genome,” Science, vol. 305, no. 5683, pp. 525–528, 2004. View at Publisher · View at Google Scholar · View at Scopus
  4. J. L. Freeman, G. H. Perry, L. Feuk et al., “Copy number variation: new insights in genome diversity,” Genome Research, vol. 16, no. 8, pp. 949–961, 2006. View at Publisher · View at Google Scholar · View at Scopus
  5. R. Redon, S. Ishikawa, K. R. Fitch et al., “Global variation in copy number in the human genome,” Nature, vol. 444, no. 7118, pp. 444–454, 2006. View at Publisher · View at Google Scholar · View at Scopus
  6. D. F. Conrad, D. Pinto, R. Redon et al., “Origins and functional impact of copy number variation in the human genome,” Nature, vol. 464, no. 7289, pp. 704–712, 2010. View at Publisher · View at Google Scholar · View at Scopus
  7. B. E. Stranger, M. S. Forrest, M. Dunning et al., “Relative impact of nucleotide and copy number variation on gene expression phenotypes,” Science, vol. 315, no. 5813, pp. 848–853, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. J. Sebat, B. Lakshmi, D. Malhotra et al., “Strong association of de novo copy number mutations with autism,” Science, vol. 316, no. 5823, pp. 445–449, 2007. View at Publisher · View at Google Scholar · View at Scopus
  9. T. Walsh, J. M. McClellan, S. E. McCarthy et al., “Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia,” Science, vol. 320, no. 5875, pp. 539–543, 2008. View at Publisher · View at Google Scholar · View at Scopus
  10. C. E. G. Bruder, A. Piotrowski, A. A. C. J. Gijsbers et al., “Phenotypically concordant and discordant monozygotic twins display different DNA copy number variation profiles,” The American Journal of Human Genetics, vol. 82, no. 3, pp. 763–771, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. M. M. Mitchell, R. Woods, L.-H. Chi et al., “Levels of select PCB and PBDE congeners in human postmortem brain reveal possible environmental involvement in 15q11-q13 duplication autism spectrum disorder,” Environmental and Molecular Mutagenesis, vol. 53, no. 8, pp. 589–598, 2012. View at Publisher · View at Google Scholar · View at Scopus
  12. M. F. Arlt, J. G. Mulle, V. M. Schaibley et al., “Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants,” American Journal of Human Genetics, vol. 84, no. 3, pp. 339–350, 2009. View at Publisher · View at Google Scholar · View at Scopus
  13. M. F. Arlt, A. C. Ozdemir, S. R. Birkeland, T. E. Wilson, and T. W. Glover, “Hydroxyurea induces de novo copy number variants in human cells,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 42, pp. 17360–17365, 2011. View at Publisher · View at Google Scholar · View at Scopus
  14. M. F. Arlt, S. Rajendran, S. R. Birkeland, T. E. Wilson, and T. W. Glover, “Copy number variants are produced in response to low-dose ionizing radiation in cultured cells,” Environmental and Molecular Mutagenesis, vol. 55, no. 2, pp. 103–113, 2014. View at Publisher · View at Google Scholar · View at Scopus
  15. C. L. Yauk, J. Lucas Argueso, S. S. Auerbach et al., “Harnessing genomics to identify environmental determinants of heritable disease,” Mutation Research—Reviews in Mutation Research, vol. 752, no. 1, pp. 6–9, 2013. View at Publisher · View at Google Scholar · View at Scopus
  16. W. B. Barbazuk, I. Korf, C. Kadavi et al., “The syntenic relationship of the zebrafish and human genomes,” Genome Research, vol. 10, no. 9, pp. 1351–1358, 2000. View at Publisher · View at Google Scholar · View at Scopus
  17. K. Howe, M. D. Clark, C. F. Torroja et al., “The zebrafish reference genome sequence and its relationship to the human genome,” Nature, vol. 496, no. 7446, pp. 498–503, 2013. View at Publisher · View at Google Scholar
  18. J. F. Amatruda and L. I. Zon, “Dissecting hematopoiesis and disease using the zebrafish,” Developmental Biology, vol. 216, no. 1, pp. 1–15, 1999. View at Publisher · View at Google Scholar · View at Scopus
  19. K. Dooley and L. I. Zon, “Zebrafish: a model system for the study of human disease,” Current Opinion in Genetics and Development, vol. 10, no. 3, pp. 252–256, 2000. View at Publisher · View at Google Scholar · View at Scopus
  20. A. J. Hill, H. Teraoka, W. Heideman, and R. E. Peterson, “Zebrafish as a model vertebrate for investigating chemical toxicity,” Toxicological Sciences, vol. 86, no. 1, pp. 6–19, 2005. View at Publisher · View at Google Scholar · View at Scopus
  21. C. L. Bladen, S. Navarre, W. S. Dynan, and D. J. Kozlowski, “Expression of the Ku70 subunit (XRCC6) and protection from low dose ionizing radiation during zebrafish embryogenesis,” Neuroscience Letters, vol. 422, no. 2, pp. 97–102, 2007. View at Publisher · View at Google Scholar · View at Scopus
  22. K. H. Brown, K. P. Dobrinski, A. S. Lee et al., “Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 2, pp. 529–534, 2012. View at Publisher · View at Google Scholar · View at Scopus
  23. J. L. Freeman, A. Adeniyi, R. Banerjee et al., “Definition of the zebrafish genome using flow cytometry and cytogenetic mapping,” BMC Genomics, vol. 8, article 195, 2007. View at Publisher · View at Google Scholar · View at Scopus
  24. M. J. Plewa, Y. Kargalioglu, D. Vankerk, R. A. Minear, and E. D. Wagner, “Mammalian cell cytotoxicity and genotoxicity analysis of drinking water disinfection by-products,” Environmental and Molecular Mutagenesis, vol. 40, no. 2, pp. 134–142, 2002. View at Publisher · View at Google Scholar · View at Scopus
  25. S. M. Peterson and J. L. Freeman, “Cancer cytogenetics in the zebrafish,” Zebrafish, vol. 6, no. 4, pp. 355–360, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. J. L. Freeman, C. Ceol, H. Feng et al., “Construction and application of a zebrafish array comparative genomic hybridization platform,” Genes Chromosomes and Cancer, vol. 48, no. 2, pp. 155–170, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. C. Workman, L. J. Jensen, H. Jarmer et al., “A new non-linear normalization method for reducing variability in DNA microarray experiments,” Genome Biology, vol. 3, no. 9, pp. 1–16, 2002. View at Google Scholar
  28. S. M. Peterson, J. Zhang, G. Weber, and J. L. Freeman, “Global gene expression analysis reveals dynamic and developmental stage-dependent enrichment of lead-induced neurological gene alterations,” Environmental Health Perspectives, vol. 119, no. 5, pp. 615–621, 2011. View at Publisher · View at Google Scholar · View at Scopus
  29. B. M. Bolstad, R. A. Irizarry, M. Åstrand, and T. P. Speed, “A comparison of normalization methods for high density oligonucleotide array data based on variance and bias,” Bioinformatics, vol. 19, no. 2, pp. 185–193, 2003. View at Publisher · View at Google Scholar · View at Scopus
  30. R. A. Irizarry, B. Hobbs, F. Collin et al., “Exploration, normalization, and summaries of high density oligonucleotide array probe level data,” Biostatistics, vol. 4, no. 2, pp. 249–264, 2003. View at Publisher · View at Google Scholar · View at Scopus
  31. L. Guo, E. K. Lobenhofer, C. Wang et al., “Rat toxicogenomic study reveals analytical consistency across microarray platforms,” Nature Biotechnology, vol. 24, no. 9, pp. 1162–1169, 2006. View at Publisher · View at Google Scholar · View at Scopus
  32. L. Shi, L. H. Reid, W. D. Jones et al., “The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements,” Nature Biotechnology, vol. 24, no. 9, pp. 1151–1161, 2006. View at Publisher · View at Google Scholar
  33. P. F. Swann and P. N. Magee, “Nitrosamine-induced carcinogenesis. The alkylation of N-7 of guanine of nucleic acids of the rat by diethylnitrosamine, N-ethyl-N-nitrosourea and ethyl methanesulphonate,” Biochemical Journal, vol. 125, no. 3, pp. 841–847, 1971. View at Google Scholar · View at Scopus
  34. K. Mogami, P. T. O'Donnell, S. I. Bernstein, T. R. Wright, and C. P. Emerson Jr., “Mutations of the Drosophila myosin heavy-chain gene: effects on transcription, myosin accumulation, and muscle function,” Proceedings of the National Academy of Sciences of the United States of America, vol. 83, no. 5, pp. 1393–1397, 1986. View at Publisher · View at Google Scholar · View at Scopus
  35. S. G. Whittaker, S. F. Moser, D. H. Maloney, W. W. Piegorsch, M. A. Resnick, and S. Fogel, “The detection of mitotic and meiotic chromosome gain in the yeast Saccharomyces cerevisiae: effects of methyl benzimidazol-2-yl carbamate, methyl methanesulfonate, ethyl methanesulfonate, dimethyl sulfoxide, propionitrile and cyclophosphamide monohydrate,” Mutation Research/Genetic Toxicology, vol. 242, no. 3, pp. 231–258, 1990. View at Publisher · View at Google Scholar · View at Scopus
  36. J. L. Freeman and A. L. Rayburn, “In vivo genotoxicity of atrazine to anuran larvae,” Mutation Research—Genetic Toxicology and Environmental Mutagenesis, vol. 560, no. 1, pp. 69–78, 2004. View at Publisher · View at Google Scholar · View at Scopus
  37. G. E. Pantelias and S. Wolff, “Cytosine arabinoside is a potent clastogen and does not affect the repair of X-ray-induced chromosome fragments in unstimulated human lymphocytes,” Mutation Research, vol. 151, no. 1, pp. 65–72, 1985. View at Publisher · View at Google Scholar · View at Scopus
  38. F. M. Elli, L. De Sanctis, E. Peverelli et al., “Autosomal dominant pseudohypoparathyroidism type Ib: a novel inherited deletion ablating STX16 causes loss of imprinting at the A/B DMR,” Journal of Clinical Endocrinology and Metabolism, vol. 99, no. 4, pp. E724–E728, 2014. View at Publisher · View at Google Scholar · View at Scopus
  39. A. Linge, S. Kennedy, D. O'Flynn et al., “Differential expression of fourteen proteins between uveal melanoma from patients who subsequently developed distant metastases versus those who did not,” Investigative Ophthalmology and Visual Science, vol. 53, no. 8, pp. 4634–4643, 2012. View at Publisher · View at Google Scholar · View at Scopus
  40. M. Emerenciano, T. C. Barbosa, B. A. Lopes et al., “ARID5B polymorphism confers an increased risk to acquire specific MLL rearrangements in early childhood leukemia,” BMC Cancer, vol. 14, no. 1, article 127, 2014. View at Publisher · View at Google Scholar · View at Scopus
  41. V. B. Mahajan and J. H. Lin, “Lymphocyte infiltration in CAPN5 autosomal dominant neovascular inflammatory vitreoretinopathy,” Clinical Ophthalmology, vol. 7, pp. 1339–1345, 2013. View at Publisher · View at Google Scholar · View at Scopus
  42. T. Franz, L. Winckler, T. Boehm, and T. N. Dear, “Capn5 is expressed in a subset of T cells and is dispensable for development,” Molecular and Cellular Biology, vol. 24, no. 4, pp. 1649–1654, 2004. View at Publisher · View at Google Scholar · View at Scopus
  43. C. N. Henrichsen, E. Chaignat, and A. Reymond, “Copy number variants, diseases and gene expression,” Human Molecular Genetics, vol. 18, no. 1, pp. R1–R8, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. I. G. Woods, C. Wilson, B. Friedlander et al., “The zebrafish gene map defines ancestral vertebrate chromosomes,” Genome Research, vol. 15, no. 9, pp. 1307–1314, 2005. View at Publisher · View at Google Scholar · View at Scopus