Selection of Reference Genes for qPCR- And ddPCR-Based Analyses of Gene Expression in Senescing Barley Leaves

PLoS ONE

Volumn 10, Issue 2, 2015, Pages

  Zmienko, Agnieszka ^a,b   Samelak Czajka, Anna ^b   Goralski, Michal ^a   Sobieszczuk Nowicka, Ewa ^c   Kozlowski, Piotr ^a   Figlerowicz, Marek ^a,b  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^b POZNAN UNIVERSITY OF TECHNOLOGY   (Poland)

^c ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; MICRORNA; MICRORNA 135B; MICRORNA 141; MICRORNA 16; MICRORNA 205; MICRORNA 210; MICRORNA 375; UNCLASSIFIED DRUG;

AGXT GENE; ARTICLE; BARLEY; CELL ULTRASTRUCTURE; CS GENE; DOWN REGULATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE NUMBER; GENE TARGETING; GENETIC VARIABILITY; ICL GENE; LEAF SENESCENCE; MARKER GENE; NONHUMAN; PLANT GENE; PLANT LEAF; RBCS GENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SAG12 GENE; UPREGULATION; GENE EXPRESSION REGULATION; GENETICS; HORDEUM; POLYMERASE CHAIN REACTION; PROCEDURES; REPRODUCIBILITY; RNA STABILITY; SENSITIVITY AND SPECIFICITY; TIME;

HORDEUM;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; HORDEUM; PLANT LEAVES; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RNA STABILITY; SENSITIVITY AND SPECIFICITY; TIME FACTORS;

EID: 84923831453     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0118226     Document Type: Article

References (42)

1. Bustin SA, Beaulieu JF, Huggett J, Jaggi R, Kibenge FS, et al. (2010) MIQE précis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments. BMC Mol Biol 11:74. doi: 10.1186/1471-2199-11-74 PMID: 20858237
2. Tricarico C, Pinzani P, Bianchi S, Paglierani M, Distante V, et al. (2002) Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal Biochem 309: 293-300. PMID: 12413463
3. Dheda K, Huggett JF, Bustin SA, Johnson MA, Rook G, et al. (2004) Validation of housekeeping genes for normalizing RNA expression in real-time PCR. Biotechniques 37: 112-119. PMID: 15283208
4. Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, et al. (2005) The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Anal Biochem 344: 141-143. PMID: 16054107
5. Huggett J, Dheda K, Bustin S, Zumla A (2005) Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 6: 279-284. PMID: 15815687
6. Baker M (2012) Digital PCR hits its stride. Nat Methods 9: 541-544.
7. Day E, Dear PH, McCaughan F (2013) Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine. Methods 59: 101-107. doi: 10.1016/j.ymeth.2012.08.001 PMID: 22926236
8. Vogelstein B, Kinzler K (1999) Digital PCR. Proc Natl Acad Sci USA 96: 9236-9241. PMID: 10430926
9. Belzil VV, Bauer PO, Prudencio M, Gendron TF, Stetler CT, et al. (2013) Reduced C9orf72 gene expression in c9FTD/ALS is caused by histone trimethylation, an epigenetic event detectable in blood. Acta Neuropathol 126: 895-905. doi: 10.1007/s00401-013-1199-1 PMID: 24166615
10. Heredia NJ, Belgrader P, Wang S, Koehler R, Regan J, et al. (2013) Droplet Digital PCR quantitation of HER2 expression in FFPE breast cancer samples. Methods 59: S20-S23. doi: 10.1016/j.ymeth.2012.09.012 PMID: 23036330
11. Beliakova-Bethell N, Jain S, Woelk CH, Witt MD, Sun X, et al. (2014) Maraviroc intensification in patients with suppressed HIV viremia has limited effects on CD4+ T cell recovery and gene expression. Antiviral Res 107: 42-49. doi: 10.1016/j.antiviral.2014.04.005 PMID: 24769244
12. Iyer CC, McGovern VL, Wise DO, Glass DJ, Burghes AH (2014) Deletion of atrophy enhancing genes fails to ameliorate the phenotype in a mouse model of spinal muscular atrophy. Neuromuscul Disord 24: 436-444. doi: 10.1016/j.nmd.2014.02.007 PMID: 24656734
13. Li N, Ma J, Guarnera MA, Fang H, Cai L, et al. (2014) Digital PCR quantification of miRNAs in sputum for diagnosis of lung cancer. J Cancer Res Clin Oncol 140: 145-150. doi: 10.1007/s00432-013-1555-5 PMID: 24281335
14. Dodd DW, Gagnon KT, Corey DR (2013) Digital quantitation of potential therapeutic target RNAs. Nucleic Acid Ther 23: 188-194. doi: 10.1089/nat.2013.0427 PMID: 23656494
15. Hindson CM, Chevillet JR, Briggs HA, Gallichotte EN, Ruf IK, et al. (2013) Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat Methods 10: 1003-1005. doi: 10.1038/nmeth.2633 PMID: 23995387
16. Huggett JF, Foy CA, Benes V, Emslie K, Garson JA, et al. (2013) Guidelines for Minimum Information for Publication of Quantitative Digital PCR Experiments. Clin Chem 59: 892-902. doi: 10.1373/clinchem.2013.206375 PMID: 23570709
17. Thomas H, Ougham HJ, Wagstaff C and Stead AD (2003) Defining senescence and death. J Exp Bot 54:1127-1132. PMID: 12654863
18. Buchanan-Wollaston V, Earl S, Harrison E, Mathas E, Navabpou S, et al. (2003) The molecular analysis of plant senescence - a genomics approach. Plant Biotechnol J 1:3-22. PMID: 17147676
19. Gregersen P, Holm PB, Krupinska K (2008) Leaf senescence and nutrient remobilisation in barley and wheat. Plant Biol 10: 37-49. doi: 10.1111/j.1438-8677.2008.00114.x PMID: 18721310
20. Fukao T, Yeung E, Bailey-Serres J (2012) The submergence tolerance gene SUB1A delays leaf senescence under prolonged darkness through hormonal regulation in rice. Plant Physiol 160: 1795-1807. doi: 10.1104/pp.112.207738 PMID: 23073696
21. Engqvist MK, Kuhn A, Wienstroer J, Weber K, Jansen EE, et al. (2011) Plant D-2-hydroxyglutarate dehydrogenase participates in the catabolism of lysine especially during senescence. J Biol Chem 286: 11382-11390. doi: 10.1074/jbc.M110.194175 PMID: 21296880
22. Kim JI, Murphy AS, Baek D, Lee SW, Yun DJ, et al. (2011) YUCCA6 over-expression demonstrates auxin function in delaying leaf senescence in Arabidopsis thaliana. J Exp Bot 62: 3981-3992. doi: 10.1093/jxb/err094 PMID: 21511905
23. Von Saint Paul V, Zhang W, Kanawati B, Geist B, Faus-Kessler T, et al. (2011) The Arabidopsis glucosyltransferase UGT76B1 conjugates isoleucic acid and modulates plant defense and senescence. Plant Cell 23: 4124-4145. doi: 10.1105/tpc.111.088443 PMID: 22080599
24. Yang SD, Seo PJ, Yoon HK, Park CM (2011) The Arabidopsis NAC transcription factor VNI2 integrates abscisic acid signals into leaf senescence via the COR/RD genes. Plant Cell 23: 2155-2168. doi: 10.1105/tpc.111.084913 PMID: 21673078
25. Evans T, Song J, Jameson PE (2012) Micro-scale chlorophyll analysis and developmental expression of a cytokinin oxidase/dehydrogenase gene during leaf development and senescence. Plant Growth Regul 66: 95-99.
26. Christiansen MW, Gregersen PL (2014) Members of the barley NAC transcription factor gene family show differential co-regulation with senescence-associated genes during senescence of flag leaves. J Exp Bot 65: 4009-4022. doi: 10.1093/jxb/eru046 PMID: 24567495
27. Fernandez P, Di Rienzo JA, Moschen S, Dosio GA, Aguirrezábal LA, et al. (2011) Comparison of predictive methods and biological validation for qPCR reference genes in sunflower leaf senescence transcript analysis. Plant Cell Rep 30: 63-74. doi: 10.1007/s00299-010-0944-3 PMID: 21076836
28. Czechowski T, Stiit M, Atlmann T, Udvardi M, Scheible W (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139: 5-17. PMID: 16166256
29. Coito JL, Rocheta M, Carvalho L, Amâncio S (2012) Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress. BMC Res Notes 5:220. doi: 10.1186/1756-0500-5-220 PMID: 22564373
30. Zhao DJ, Guo K, Kang L (2012) Identification of condition-specific reference genes from microarray data for locusts exposed to hypobaric hypoxia. FEBS Open Bio 2: 235-240. doi: 10.1016/j.fob.2012.08.001 PMID: 23650605
31. Chan PL, Rose RJ, Murad AMA, Zainal Z, Low ETL, et al. (2014) Evaluation of reference genes for quantitative real-time PCR in oil palm elite planting materials propagated by tissue culture. PLoS One 9: e99774. doi: 10.1371/journal.pone.0099774 PMID: 24927412
32. Hruz T, Wyss M, Docquier M, Pfaffl MW, Masanetz S, et al. (2011) RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization. BMC Genomics 12: 156. doi: 10.1186/1471-2164-12-156 PMID: 21418615
33. Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R and Huber W, editors. Bioinformatics and Computational Biology Solutions Using R and Bioconductor, New York: Springer. pp. 397-420.
34. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, et al. (2011) NCBI GEO: archive for functional genomics data sets - 10 years on. Nucleic Acids Res 39: D1005-D1010. doi: 10.1093/nar/gkq1184 PMID: 21097893
35. Breeze E, Harrison E, McHattie S, Hughes L, Hickman R, et al. (2011) High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell 23: 873-894. doi: 10.1105/tpc.111.083345 PMID: 21447789
36. Kulik A, Anielska-Mazur A, Bucholc M, Koen E, Szymanska K, et al. (2012) SNF1-related protein kinases type 2 are involved in plant responses to cadmium stress. Plant Physiol: 160: 868-883. doi: 10.1104/pp.112.194472 PMID: 22885934
37. McDermott GP, Do D, Litterst CM, Maar D, Hindson CM, et al. (2013) Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR. Anal Chem 85: 11619-11627. doi: 10.1021/ac403061n PMID: 24180464
38. Legocka J, Szweykowska A (1981) The role of cytokinins in the development and metabolism of barley leaves III. The effect on the RNA metabolism in various cell compartments during senescence. Z Pflanzenphysiol 102: 363-374.
39. Jackowski G (1996) Senescence-related changes in the subcomplex arrangement of the major light-harvesting chlorophyll a/b-protein complex of photosystem II (LHCII) as influenced by cytokinin. Z Naturforschung 51: 464-472.
40. Żelisko A, Jackowski G (2004) Senescence-dependent degradation of Lhcb3 is mediated by a thylakoid membrane-bound protease. J Plant Physiol 161: 1157-1170. PMID: 15535125
41. Sobieszczuk-Nowicka E, Wieczorek P, Legocka J (2009) Kinetin affects the level of chloroplast polyamines and transglutaminase activity during senescence of barley leaves. Acta Biochim Pol 56: 255-259. PMID: 19436838
42. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: research0034.1-research0034.11.