Lựa chọn các gen tham chiếu đáng tin cậy cho nghiên cứu biểu hiện gen ở đào bằng phương pháp PCR thời gian thực
Tóm tắt
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Tài liệu tham khảo
Ginzinger DG: Gene quantification using real-time quantitative PCR: An emerging technology hits the mainstream. Exp Hematol. 2002, 30 (6): 503-512.
Bustin SA: Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol. 2002, 29 (1): 23-39.
Garson JA, Grant PR, Ayliffe U, Ferns RB, Tedder RS: Real-time PCR quantitation of hepatitis B virus DNA using automated sample preparation and murine cytomegalovirus internal control. J Virol Methods. 2005, 126 (1–2): 207-213.
Huggett J, Dheda K, Bustin S, Zumla A: Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005, 6 (4): 279-284.
Schmittgen TD, Zakrajsek BA: Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR. J Biochem Biophys Methods. 2000, 46 (1–2): 69-81.
Thellin O, Zorzi W, Lakaye B, De Borman B, Coumans B, Hennen G, Grisar T, Igout A, Heinen E: Housekeeping genes as internal standards: use and limits. J Biotechnol. 1999, 75 (2–3): 291-295.
Cappelli K, Felicetti M, Capomaccio S, Spinsanti G, Silvestrelli M, Supplizi AV: Exercise induced stress in horses: selection of the most stable reference genes for quantitative RT-PCR normalization. BMC Mol Biol. 2008, 9: 49-
Dheda K, Huggett J, Bustin SA, Johnson MA, Rook G, Zumla A: Validation of housekeeping genes for normalizing RNA expression in real-time PCR. BioTechniques. 2004, 37: 112-119.
Suzuki T, Higgins PJ, DR C: Control selection for RNA quantitation. BioTechniques. 2000, 29: 332-337.
Bas A, Forsberg G, Hammarstrom S, Hammarstrom ML: Utility of the housekeeping genes 18S rRNA, beta-actin and glyceraldehyde-3-phosphate-dehydrogenase for normalization in real-time quantitative reverse transcriptase-polymerase chain reaction analysis of gene expression in human T lymphocytes. Scand J Immunol. 2004, 59 (6): 566-573.
Yperman J, De Visscher G, Holvoet P, Flameng W: Beta-actin cannot be used as a control for gene expression in ovine interstitial cells derived from heart valves. J Heart Valve Dis. 2004, 13 (5): 848-853.
Barber RD, Harmer DW, Coleman RA, Clark BJ: GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues. Physiol Genomics. 2005, 21 (3): 389-395.
Nicot N, Hausman JF, Hoffmann L, Evers D: Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot. 2005, 56 (421): 2907-2914.
Ishitani R, Sunaga K, Hirano A, Saunders P, Katsube N, Chuang DM: Evidence that glyceraldehyde-3-phosphate dehydrogenase is involved in age-induced apoptosis in mature cerebellar neurons in culture. J Neurochem. 1996, 66 (3): 928-935.
Singh R, Green M: Sequence-specific binding of transfer RNA by glyceraldehyde-3-phosphate dehydrogenase. Science. 1993, 259 (5093): 365-368.
Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, Johnson MA, Rook GAW, Zumla A: The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Anal Biochem. 2005, 344 (1): 141-143.
Tatsumi K, Ohashi K, Taminishi S, Okano T, Yoshioka A, Shima M: Reference gene selection for real-time RT-PCR in regenerating mouse livers. Biochem Biophys Res Commun. 2008, 374 (1): 106-110.
Paolacci A, Tanzarella O, Porceddu E, Ciaffi M: Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC molecular biology. 2009, 10 (1): 11-
Burton RA, Shirley NJ, King BJ, Harvey AJ, Fincher GB: The CesA Gene Family of Barley. Quantitative Analysis of Transcripts Reveals Two Groups of Co-Expressed Genes. Plant Physiol. 2004, 134 (1): 224-236.
Ding J, Jia J, Yang L, Wen H, Zhang C, Liu W, Zhang D: Validation of a rice specific gene, sucrose phosphate synthase, used as the endogenous reference gene for qualitative and real-time quantitative PCR detection of transgenes. J Agric Food Chem. 2004, 52 (11): 3372-3377.
Jain M, Nijhawan A, Tyagi AK, Khurana JP: Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun. 2006, 345 (2): 646-651.
Kim BR, Nam HY, Kim SU, Kim SI, Chang YJ: Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett. 2003, 25 (21): 1869-1872.
Jian B, Liu B, Bi Y, Hou W, Wu C, Han T: Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol. 2008, 9 (1): 59-
Reid KE, Olsson N, Schlosser J, Peng F, Lund ST: An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biol. 2006, 6 (1): 27-
Brunner AM, Yakovlev IA, Strauss SH: Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol. 2004, 4 (1): 14-
Coker JS, Davies E: Selection of candidate housekeeping controls in tomato plants using EST data. BioTechniques. 2003, 35: 740-748.
Exposito-Rodriguez M, Borges A, Borges-Perez A, Perez J: Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biology. 2008, 8 (1): 131-
Barsalobres-Cavallari C, Severino F, Maluf M, Maia I: Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC molecular biology. 2009, 10 (1): 1-
Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible W-R: Genome-wide identification and testing of superior reference genes for transcript normalization in arabidopsis. Plant Physiol. 2005, 139 (1): 5-17.
Remans T, Smeets K, Opdenakker K, Mathijsen D, Vangronsveld J, Cuypers A: Normalisation of real-time RT-PCR gene expression measurements in arabidopsis thaliana exposed to increased metal concentrations. Planta. 2008, 227 (6): 1343-1349.
Fischer RL, Bennett AB: Role of cell wall hydrolases in fruit ripening. Plant Mol Biol. 1991, 42: 675-703.
Fonseca S, Hackler L, Zvara Á, Ferreira S, Bald A, Dudits D, Pais MS, Puskás LG: Monitoring gene expression along pear fruit development, ripening and senescence using cDNA microarrays. Plant Sci. 2004, 167 (3): 457-469.
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 (7): RESEARCH0034-
Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP: Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations. Biotechnol Lett. 2004, 26 (6): 509-515.
Andersen CL, Jensen JL, Orntoft TF: 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 (15): 5245-5250.
Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT: The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009, 55 (4): 611-622.
geNorm Software. http://medgen.ugent.be/~jvdesomp/genorm/
Tricarico C, Pinzani P, Bianchi S, Paglierani M, Distante V, Pazzagli M, Bustin SA, Orlando C: Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal Biochem. 2002, 309 (2): 293-300.
Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J: qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007, 8: R19-
García-Vallejo JJ, Van het Hof B, Robben J, Van Wijk JAE, Van Die I, Joziasse DH, Van Dijk W: Approach for defining endogenous reference genes in gene expression experiments. Anal Biochem. 2004, 329 (2): 293-299.
Haller F, Kulle B, Schwager S, Gunawan B, Heydebreck Av, Sültmannd H, Füzesi L: Equivalence test in quantitative reverse transcription polymerase chain reaction: confirmation of reference genes suitable for normalization. Anal Biochem. 2004, 335 (1): 1-9.
Brunner AM, Yakovlev IA, Strauss SH: Validating internal controls for quantitative plant gene expression studies. BMC Plant Biology. 2004, 4 (1): 14-
Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A: Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun. 2004, 313 (4): 856-862.
de Kok JB, Roelofs RW, Giesendorf BA, Pennings JL, Waas ET, Feuth T, Swinkels DW, Span PN: Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Invest. 2005, 85 (1): 154-159.
Szabo A, Perou CM, Karaca M, Perreard L, Palais R, Quackenbush JF, Bernard PS: Statistical modeling for selecting housekeeper genes. Genome Biol. 2004, 5 (8): R59-
Ayers D, Clements D, Salway F, Day P: Expression stability of commonly used reference genes in canine articular connective tissues. BMC Veterinary Research. 2007, 3: 7-
Løvdal T, Lillo C: Reference gene selection for quantitative real-time PCR normalization in tomato subjected to nitrogen, cold, and light stress. Analytical Biochemistry. 2009, 387 (2): 238-242.
Hochstrasser M: Evolution and function of ubiquitin-like protein-conjugation systems. Nat Cell Biol. 2000, 2 (8): E153-157.
Marivet J, Frendo P, Burkard G: Effects of antibiotic stresses on cyclophilin in maize and bean and sequence analysis of bean cyclophilin cDNA. Plant Sci. 1992, 84: 171-178.
Iskandar H, Simpson R, Casu R, Bonnett G, Maclean D, Manners J: Comparison of reference genes for quantitative real-time polymerase chain reaction analysis of gene expression in sugarcane. Plant Mol Biol Rep. 2004, 22 (4): 325-337.
Gonzalez-Verdejo CI, Die JV, Nadal S, Jimenez-Marin A, Moreno MT, Roman B: Selection of housekeeping genes for normalization by real-time RT-PCR: analysis of Or-MYB1 gene expression in orobanche ramosa development. Anal Biochem. 2008, 379 (2): 176-181.
RT-PCR: The basic. http://www.ambion.com/techlib/basics/rtpcr/index.html
Takle GW, K TI, Brurberg MB: Evaluation of reference genes for real-time RT-PCR expression studies in the plant pathogen pectobacterium atrosepticum. BMC Plant Biol. 2007, 7: 50-
Vera MI, Norambuena L, Alvarez M, Figueroa J, Molina A, Leon G, Krauskopf M: Reprogramming of nucleolar gene expression during the acclimatization of the carp. Cell Mol Biol Res. 1993, 39 (7): 665-674.
Stürzenbaum SR, Kille P: Control genes in quantitative molecular biological techniques: the variability of invariance. Comp Biochem Phys B: Biochem Mol Biol. 2001, 130 (3): 281-289.
Gutierrez L, Mauriat M, Guenin S, Pelloux J, Lefebvre JF, Louvet R, Rusterucci C, Moritz T, Guerineau F, Bellini C, Van Wuytswinkel O: The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol J. 2008, 609-618. 6
Begheldo M, Ziliotto F, Rasori A, Bonghi C: The use of μPEACH 1.0 to investigate the role of ethylene in the initiation of peach fruit ripening. Advances in Plant Ethylene Research. 2007, 265-267.
Ziosi V, Bonghi C, Bregoli AM, Trainotti L, Biondi S, Sutthiwal S, Kondo S, Costa G, Torrigiani P: Jasmonate-induced transcriptional changes suggest a negative interference with the ripening syndrome in peach fruit. J Exp Bot. 2008, 59 (3): 563-573.
Liguori G, Weksler A, Zutahi Y, Lurie S, Kosto I: Effect of 1-methylcyclopropene on ripening of melting flesh peaches and nectarines. Postharvest Biol Tec. 2004, 31 (3): 263-268.
Trainotti L, Pavanello A, Zanin D: PpEG4 is a peach endo-beta-1, 4-glucanase gene whose expression in climacteric peaches does not follow a climacteric pattern. J Exp Bot. 2006, 57 (3): 589-598.
Meisel L, Fonseca B, González S, Baezayates R, Cambiazo V, Campos R, Gonzalez M, Orellana A, Retamales J, Silva H: A rapid and efficient method for purifying high quality total RNA from peaches (Prunus persica) for functional genomics analyses. Biol Res. 2005, 38: 83-88.
Peach EST database. http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=peach
TAIR BLAST. http://www.arabidopsis.org/Blast/index.jsp
Fleige S, MW P: RNA integrity and the effect on the realtime qRT-PCR performance. Mol Aspects Med. 2006, 27: 126-139.
Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31 (13): 3406-3415.
Ramakers C, Ruijter JM, Deprez RH, Moorman AF: Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett. 2003, 339 (1): 62-66.
Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods. 2001, 25 (4): 402-408.
NormFinder Software. http://www.mdl.dk/publicationsnormfinder.htm
BestKeeper Software. http://www.gene-quantification.de/bestkeeper.html