Abstract
Among vertebrates, the mammalian systems that are frequently used to investigate questions related to human health have gained the most benefit from microarray technology to date. However, it is clear that biological investigations and the generalized conclusions drawn from them, can only be enhanced by including organisms in which specific processes can be readily studied because of their genetic, physiological, or developmental disposition. As a result, the field of functional genomics has recently begun to embrace a number of other vertebrate species. This review summarizes the current state of microarray technology in a subset of these vertebrate organisms, including Xenopus, Rana, zebrafish, killifish (Fundulus sp.), medaka (Oryzias latipes), Atlantic salmon, and rainbow trout. A summary of various applications of microarray technology and a brief introduction to the steps involved in carrying out a microarray experiment are also presented.
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References
Oleksiak, M. F., Kolell, K. J., and Crawford, D. L. (2001) Utility of natural populations for microarray analyses: isolation of genes necessary for functional genomic studies. Mar. Biotechnol. (NY) 3, S203–S211.
Renn, S. C., Aubin-Horth, N., and Hofmann, H. A. (2004) Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics 5, 42.
Levine, M. and Davidson, E. H. (2005) Gene regulatory networks for development. Proc. Natl. Acad. Sci. USA 102, 4936–4942.
Pollet, N., Muncke, N., Verbeek, B., et al. (2005) An atlas of differential gene expression during early Xenopus embryogenesis. Mech. Dev. 122, 365–439.
Kudoh, T., Tsang, M., Hukriede, N. A., et al. (2001) A gene expression screen in zebrafish embryogenesis. Genome Res. 11, 1979–1987.
Quiring, R., Wittbrodt, B., Henrich, T., et al. (2004) Large-scale expression screening by automated whole-mount in situ hybridization. Mech. Dev. 121, 971–976.
Baldessari, D., Shin, Y., Krebs, O., et al. (2005) Global gene expression profiling and cluster analysis in Xenopus laevis. Mech. Dev. 122, 441–475.
Ton, C., Stamatiou, D., Dzau, V. J., and Liew, C. C. (2002) Construction of a zebrafish cDNA microarray: gene expression profiling of the zebrafish during development. Biochem. Biophys. Res. Commun. 296, 1134–1142.
Lo, J., Lee, S., Xu, M., et al. (2003) 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome Res. 13, 455–466.
Linney, E., Dobbs-McAuliffe, B., Sajadi, H., and Malek, R. L. (2004) Microarray gene expression profiling during the segmentation phase of zebrafish development. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 138, 351–362.
Kimura, T., Jindo, T., Narita, T., et al. (2004) Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics. Mech. Dev. 121, 915–932.
von Schalburg, K. R., Rise, M. L., Brown, G. D., Davidson, W. S., and Koop, B. F. (2005) A comprehensive survey of the genes involved in maturation and development of the rainbow trout ovary. Biol. Reprod. 72, 687–699.
Altmann, C. R., Bell, E., Sczyrba, A., et al. (2001) Microarray-based analysis of early development in Xenopus laevis. Dev. Biol. 236, 64–75.
Vallee, M., Gravel, C., Palin, M. F., et al. (2005) Identification of novel and known oocyte-specific genes using complementary DNA subtraction and microarray analysis in three different species. Biol. Reprod. 73, 63–71.
Chung, H. A., Hyodo-Miura, J., Kitayama, A., Terasaka, C., Nagamune, T., and Ueno, N. (2004) Screening of FGF target genes in Xenopus by microarray: temporal dissection of the signalling pathway using a chemical inhibitor. Genes Cells 9, 749–761.
Arima, K., Shiotsugu, J., Niu, R., et al. (2005) Global analysis of RARresponsive genes in the Xenopus neurula using cDNA microarrays. Dev. Dyn. 232, 414–431.
Peiffer, D. A., Von Bubnoff, A., Shin, Y., et al. (2005) A Xenopus DNA microarray approach to identify novel direct BMP target genes involved in early embryonic development. Dev. Dyn. 232, 445–456.
Shin, Y., Kitayama, A., Koide, T., et al. (2005) Identification of neural genes using Xenopus DNA microarrays. Dev. Dyn. 233, 248.
Taverner, N. V., Kofron, M., Shin, Y., et al. (2005) Microarray-based identification of VegT targets in Xenopus. Mech. Dev. 122, 333–354.
Munoz-Sanjuan, I., Bell, E., Altmann, C. R., Vonica, A., and Brivanlou, A. H. (2002) Gene profiling during neural induction in Xenopus laevis: regulation of BMP signaling by post-transcriptional mechanisms and TAB3, a novel TAK1-binding protein. Development 129, 5529–5540.
Leung, A. Y., Mendenhall, E. M., Kwan, T. T., et al. (2005) Characterization of expanded intermediate cell mass in zebrafish chordin morphant embryos. Dev. Biol. 277, 235–254.
Katogi, R., Nakatani, Y., Shin-i, T., Kohara, Y., Inohaya, K., and Kudo, A. (2004) Large-scale analysis of the genes involved in fin regeneration and blastema formation in the medaka, Oryzias latipes. Mech. Dev. 121, 861–872.
Rise, M. L., Jones, S. R., Brown, G. D., von Schalburg, K. R., Davidson, W. S., and Koop, B. F. (2004) Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection. Physiol. Genomics 20, 21–35.
Tsoi, S. C., Cale, J. M., Bird, I. M., Ewart, V., Brown, L. L., and Douglas, S. (2003) Use of human cDNA microarrays for identification of differentially expressed genes in Atlantic salmon liver during Aeromonas salmonicida infection. Mar. Biotechnol. (NY) 5, 545–554.
Ewart, K. V., Belanger, J. C., Williams, J., et al. (2005) Identification of genes differentially expressed in Atlantic salmon (Salmo salar) in response to infection by Aeromonas salmonicida using cDNA microarray technology. Dev. Comp. Immunol. 29, 333–347.
Rawls, J. F., Samuel, B. S., and Gordon, J. I. (2004) Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc. Natl. Acad. Sci. USA 101, 4596–4601.
Podrabsky, J. E. and Somero, G. N. (2004) Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J. Exp. Biol. 207, 2237–2254.
Malek, R. L., Sajadi, H., Abraham, J., Grundy, M. A., and Gerhard, G. S. (2004) The effects of temperature reduction on gene expression and oxidative stress in skeletal muscle from adult zebrafish. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 138, 363–373.
Ton, C., Stamatiou, D., and Liew, C. C. (2003) Gene expression profile of zebrafish exposed to hypoxia during development. Physiol. Genomics 13, 97–106.
Krasnov, A., Koskinen, H., Pehkonen, P., Rexroad, C. E., 3rd, Afanasyev, S., and Molsa, H. (2005) Gene expression in the brain and kidney of rainbow trout in response to handling stress. BMC Genomics 6, 3.
Hogstrand, C., Balesaria, S., and Glover, C. N. (2002) Application of genomics and proteomics for study of the integrated response to zinc exposure in a nonmodel fish species, the rainbow trout. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 133, 523–535.
Wester, P. W., van der Ven, L. T. M., and Vos, J. G. (2004) Comparative toxicological pathology in mammals and fish: some examples with endocrine disrupters. Toxicology 205, 27–32.
Koskinen, H., Pehkonen, P., Vehniainen, E., et al. (2004) Response of rainbow trout transcriptome to model chemical contaminants. Biochem. Biophys. Res. Commun. 320, 745–753.
Fort, D. J., Rogers, R. L., Thomas, J. H., Buzzard, B. O., Noll, A. M., and Spaulding, C. D. (2004) Comparative sensitivity of Xenopus tropicalis and Xenopus laevis as test species for the FETAX model. J. Appl. Toxicol. 24, 443–457.
Feder, M. E. and Mitchell-Olds, T. (2003) Evolutionary and ecological functional genomics. Nat. Rev. Genet. 4, 651–657.
Stearns, S. C. and Magwene, P. (2003) The naturalist in a world of genomics. Am. Nat. 161, 171–180.
Oleksiak, M. F., Churchill, G. A., and Crawford, D. L. (2002) Variation in gene expression within and among natural populations. Nat. Genet. 32, 261–266.
Oleksiak, M. F., Roach, J. L., and Crawford, D. L. (2005) Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nat. Genet. 37, 67–72.
Chalmers, A. D., Goldstone, K., Smith, J. C., Gilchrist, M., Amaya, E., and Papalopulu, N. (2005) A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis. Mech. Dev. 122, 355–363.
Rise, M. L., von Schalburg, K. R., Brown, G. D., et al. (2004) Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res. 14, 478–490.
Mori, T., Hiraka, I., Kurata, Y., Kawachi, H., Kishida, O., and Nishimura, K. (2005) Genetic basis of phenotypic plasticity for predator-induced morphological defenses in anuran tadpole, Rana pirica, using cDNA subtraction and microarray analysis. Biochem. Biophys. Res. Commun. 330, 1138–1145.
Chen, Y. A., McKillen, D. J., Wu, S., et al. (2004) Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. BMC Bioinformatics 5, 191.
Lorenz, M. G., Cortes, L. M., Lorenz, J. J., and Liu, E. T. (2003) Strategy for the design of custom cDNA microarrays. Biotechniques 34, 1264–1270.
Li, J., Pankratz, M., and Johnson, J. A. (2002) Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol. Sci. 69, 383–390.
Dondeti, V. R., Sipe, C. W., and Saha, M. S. (2004) In silico gene selection strategy for custom microarray design. Biotechniques 37, 768–770, 72, 74–76.
Bowtell, D. and Sambrook, J. (2003) DNA microarrays: a molecular cloning manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
Konig, R., Baldessari, D., Pollet, N., Niehrs, C., and Eils, R. (2004) Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design. Nucleic Acids Res. 32, E29.
Van Gelder, R. N., von Zastrow, M. E., Yool, A., Dement, W. C., Barchas, J. D., and Eberwine, J. H. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. USA 87, 1663–1667.
Eberwine, J., Yeh, H., Miyashiro, K., et al. (1992) Analysis of gene expression in single live neurons. Proc. Natl. Acad. Sci. USA 89, 3010–3014.
Cox, W. G., Beaudet, M. P., Agnew, J. Y., and Ruth, J. L. (2004) Possible sources of dye-related signal correlation bias in two-color DNA microarray assays. Anal. Biochem. 331, 243–254.
Tran, P. H., Peiffer, D. A., Shin, Y., Meek, L. M., Brody, J. P., and Cho, K. W. (2002) Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals. Nucleic Acids Res. 30, E54.
Slonim, D. K. (2002) From patterns to pathways: gene expression data analysis comes of age. Nat. Genet. 32, 502–508.
Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J., and Church, G. M. (1999) Systematic determination of genetic network architecture. Nat. Genet. 22, 281–285.
Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14,863–14,868.
Landgrebe, J., Wurst, W., and Welzl, G. (2002) Permutation-validated principal components analysis of microarray data. Genome Biol. 3, RESEARCH0019.
McShane, L. M., Shih, J. H., and Michalowska, A. M. (2003) Statistical issues in the design and analysis of gene expression microarray studies of animal models. J. Mammary Gland Biol. Neoplasia 8, 359–374.
Cui, X. and Churchill, G. A. (2003) Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 4, 210.
Whitehead, A. and Crawford, D. L. (2005) Variation in tissue-specific gene expression among natural populations. Genome Biol. 6, R13.
Tusher, V. G., Tibshirani, R., and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98, 5116–5121.
Chuaqui, R. F., Bonner, R. F., Best, C. J., et al. (2002) Post-analysis follow-up and validation of microarray experiments. Nat. Genet. 32, 509–514.
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Sipe, C.W., Saha, M.S. (2007). The Use of Microarray Technology in Nonmammalian Vertebrate Systems. In: Rampal, J.B. (eds) Microarrays. Methods in Molecular Biology, vol 382. Humana Press. https://doi.org/10.1007/978-1-59745-304-2_1
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DOI: https://doi.org/10.1007/978-1-59745-304-2_1
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