Normalization strategies for gene expression studies by real-time PCR in a marine fish species, Scophthalmus maximus

Marine Genomics

Volumn 10, Issue , 2013, Pages 17-25

  Urbatzka, R ^a   Galante Oliveira, S ^a,b   Rocha, E ^a,c   Castro, L F C ^a   Cunha, I ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b UNIVERSITY OF AVEIRO   (Portugal)

^c UNIVERSITY OF PORTO   (Portugal)

Author keywords

Normalization strategies; Peroxisome proliferator activated receptor agonists; Real time quantitative RT PCR; Reference genes; Scophthalmus maximus; Teleost fish

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA;

ANIMAL; ARTICLE; FLATFISH; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; PHYSIOLOGY; REAL TIME POLYMERASE CHAIN REACTION;

ANIMALS; DNA, COMPLEMENTARY; FLATFISHES; GENE EXPRESSION REGULATION; REAL-TIME POLYMERASE CHAIN REACTION; RNA, MESSENGER;

SCOPHTHALMIDAE; SCOPHTHALMUS MAXIMUS; TELEOSTEI;

EID: 84877664667     PISSN: 18747787     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.margen.2013.02.001     Document Type: Article

References (37)

1. Andersen C.L., Jensen J.L., Orntoft T.F. Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004, 64:5245-5250.
2. Angermueller S., Islinger M., Volkl A. Peroxisomes and reactive oxygen species, a lasting challenge. Histochem. Cell Biol. 2009, 131:459-463.
3. Banmeyer I., Marchand C., Verhaeghe C., Vucic B., Rees J.F., Knoops B. Overexpression of human peroxiredoxin 5 in subcellular compartments of Chinese hamster ovary cells: effects on cytotoxicity and DNA damage caused by peroxides. Free Radic. Biol. Med. 2004, 36:65-77.
4. Banmeyer I., Marchand C., Clippe A., Knoops B. Human mitochondrial peroxiredoxin 5 protects from mitochondrial DNA damages induced by hydrogen peroxide. FEBS Lett. 2005, 579:2327-2333.
5. Bility M.T., Thompson J.T., McKee R.H., David R.M., Butala J.H., Vanden Heuvel J.P., Peters J.M. Activation of mouse and human peroxisome proliferator-activated receptors (PPARs) by phthalate monoesters. Toxicol. Sci. 2004, 82:170-182.
6. Bustin S.A., Benes V., Nolan T., Pfaffl M.W. Quantitative real-time RT-PCR-a perspective. J. Mol. Endocrinol. 2005, 34:597-601.
7. Colliar L., Sturm A., Leaver M.J. Tributyltin is a potent inhibitor of piscine peroxisome proliferator-activated receptor alpha and beta. Comp. Biochem. Physiol. C 2011, 153:168-173.
8. Cunha I., Galante-Oliveira S., Rocha E., Planas M., Urbatzka R., Castro L.F. Dynamics of PPARs, fatty acid metabolism genes and lipid classes in eggs and early larvae of a teleost. Comp. Biochem. Physiol. B 2013, 164(4):247-258.
9. Fernandes J.M., Mommens M., Hagen O., Babiak I., Solberg C. Selection of suitable reference genes for real-time PCR studies of Atlantic halibut development. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 2008, 150:23-32.
10. Filby A.L., Tyler C.R. Appropriate 'housekeeping' genes for use in expression profiling the effects of environmental estrogens in fish. BMC Mol. Biol. 2007, 8:10.
11. Grun F., Blumberg B. Minireview: the case for obesogens. Mol. Endocrinol. 2009, 23:1127-1134.
12. Henikoff S., Henikoff J.G., Alford W.J., Pietrokovski S. Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene 1995, 163:GC17-GC26.
13. Hihi A.K., Michalik L., Wahli W. PPARs: transcriptional effectors of fatty acids and their derivatives. Cell. Mol. Life Sci. 2002, 59:790-798.
14. Huang Q., Fang C., Wu X., Fan J., Dong S. Perfluorooctane sulfonate impairs the cardiac development of a marine medaka (Oryzias melastigma). Aquat. Toxicol. 2011, 105:71-77.
15. Huggett J., Dheda K., Bustin S., Zumla A. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005, 6:279-284.
16. Hurst C.H., Waxman D.J. Activation of PPARalpha and PPARgamma by environmental phthalate monoesters. Toxicol. Sci. 2003, 74:297-308.
17. Infante C., Matsuoka M.P., Asensio E., Canavate J.P., Reith M., Manchado M. Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR. BMC Mol. Biol. 2008, 9:28.
18. Kloas W., Urbatzka R., Opitz R., Wurtz S., Behrends T., Hermelink B., Hofmann F., Jagnytsch O., Kroupova H., Lorenz C., Neumann N., Pietsch C., Trubiroha A., Van B.C., Wiedemann C., Lutz I. Endocrine disruption in aquatic vertebrates. Ann. N. Y. Acad. Sci. 2009, 1163:187-200.
19. Knoops B., Goemaere J., Van der Eecken V., Declercq J.P. Peroxiredoxin 5: structure, mechanism, and function of the mammalian atypical 2-Cys peroxiredoxin. Antioxid. Redox Signal. 2011, 15:817-829.
20. Kondo H., Misaki R., Gelman L., Watabe S. Ligand-dependent transcriptional activities of four torafugu pufferfish Takifugu rubripes peroxisome proliferator-activated receptors. Gen. Comp. Endocrinol. 2007, 154:120-127.
21. Larkin P., Knoebl I., Denslow N.D. Differential gene expression analysis in fish exposed to endocrine disrupting compounds. Comp. Biochem. Physiol. B 2003, 136:149-161.
22. Leaver M.J., Boukouvala E., Antonopoulou E., Diez A., Favre-Krey L., Ezaz M.T., Bautista J.M., Tocher D.R., Krey G. Three peroxisome proliferator-activated receptor isotypes from each of two species of marine fish. Endocrinology 2005, 146:3150-3162.
23. Libus J., Storchova H. Quantification of cDNA generated by reverse transcription of total RNA provides a simple alternative tool for quantitative RT-PCR normalization. Biotechniques 2006, 41:156-160.
24. McCurley A.T., Callard G.V. Characterization of housekeeping genes in zebrafish: male-female differences and effects of tissue type, developmental stage and chemical treatment. BMC Mol. Biol. 2008, 9:102.
25. Nguyen-Nhu N.T., Berck J., Clippe A., Duconseille E., Cherif H., Boone C., Van der Eecken V., Bernard A., Banmeyer I., Knoops B. Human peroxiredoxin 5 gene organization, initial characterization of its promoter and identification of alternative forms of mRNA. Biochim. Biophys. Acta 2007, 1769:472-483.
26. Park H., Ahn I.Y., Kim H., Cheon J., Kim M. Analysis of ESTs and expression of two peroxiredoxins in the thermally stressed Antarctic bivalve Laternula elliptica. Fish Shellfish Immunol. 2008, 25:550-559.
27. Perez-Sanchez J., Bermejo-Nogales A., Calduch-Giner J.A., Kaushik S., Sitja-Bobadilla A. Molecular characterization and expression analysis of six peroxiredoxin paralogous genes in gilthead sea bream (Sparus aurata): insights from fish exposed to dietary, pathogen and confinement stressors. Fish Shellfish Immunol. 2011, 31:294-302.
28. Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001, 29:e45.
29. Pfaffl M.W., Tichopad A., Prgomet C., Neuvians T.P. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations. Biotechnol. Lett. 2004, 26:509-515.
30. Reiser S., Wuertz S., Schroeder J.P., Kloas W., Hanel R. Risks of seawater ozonation in recirculation aquaculture - effects of oxidative stress on animal welfare of juvenile turbot (Psetta maxima, L.). Aquat. Toxicol. 2011, 105:508-517.
31. Rosal R., Rodea-Palomares I., Boltes K., Fernandez-Pinas F., Leganes F., Gonzalo S., Petre A. Ecotoxicity assessment of lipid regulators in water and biologically treated wastewater using three aquatic organisms. Environ. Sci. Pollut. Res. Int. 2010, 17:135-144.
32. Rose T.M., Schultz E.R., Henikoff J.G., Pietrokovski S., McCallum C.M., Henikoff S. Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res. 1998, 26:1628-1635.
33. Solanas M., Moral R., Escrich E. Unsuitability of using ribosomal RNA as loading control for northern blot analyses related to the imbalance between messenger and ribosomal RNA content in rat mammary tumors. Anal. Biochem. 2001, 288:99-102.
34. Urbatzka R., Lorenz C., Lutz I., Kloas W. Expression profiles of LHbeta, FSHbeta and their gonadal receptor mRNAs during sexual differentiation of Xenopus laevis tadpoles. Gen. Comp. Endocrinol. 2010, 168:239-244.
35. Vandesompele J., De Preter K., Pattyn F., Poppe B., Van Roy N., De Paepe A., Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3:1-12.
36. Zhao Y., Gul Y., Li S., Wang W. Cloning, identification and accurate normalization expression analysis of PPARalpha gene by geNorm in Megalobrama amblycephala. Fish Shellfish Immunol. 2011, 31:462-468.
37. Zheng W.J., Sun L. Evaluation of housekeeping genes as references for quantitative real time RT-PCR analysis of gene expression in Japanese flounder (Paralichthys olivaceus). Fish Shellfish Immunol. 2011, 30:638-645.