Identification of suitable endogenous control genes for quantitative RT-PCR analysis of miRNA in bovine solid tissues

Molecular Biology Reports

Volumn 41, Issue 10, 2014, Pages 6475-6480

  Li, Dongwei ^a,b,c,d   Liu, Hongyu ^a,c   Li, Yunsheng ^a,c,d   Yang, Manman ^a   Qu, Changqing ^b   Zhang, Yunhai ^a,c,d   Liu, Ya ^a,c,d   Zhang, Xiaorong ^a,c,d  

^a ANHUI AGRICULTURAL UNIVERSITY   (China)

^b FUYANG NORMAL UNIVERSITY   (China)

^c Anhui Provincial Lab for Local Livestock and Poultry Genetic Resource Conservation and Bio Breeding   (China)

^d Engineering Research Center of Reproduction and breeding in Sheep of Anhui Province   (China)

Author keywords

Bovine; Endogenous control; miRNA; Normalization; RT qPCR

Indexed keywords

GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; MICRORNA; MICRORNA 15A; MICRORNA 18A; MICRORNA 191; RNA 18S; UNCLASSIFIED DRUG; TRANSCRIPTOME;

18S RRNA GENE; ACTB GENE; ADULT; ANIMAL TISSUE; ARTICLE; CATTLE; CONTROLLED STUDY; ENDOGENOUS CONTROL GENE; GAPDH GENE; GENE; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ANALYSIS; LET 7F GENE; MICRORNA 15A GENE; MICRORNA 18A GENE; MICRORNA 191 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TISSUE SPECIFICITY; U6 GENE; VALIDATION PROCESS; ANIMAL; ANTIBODY SPECIFICITY; BOVINE; GENE EXPRESSION PROFILING; GENETICS; RNA STABILITY;

BOVINAE;

ANIMALS; CATTLE; GENE EXPRESSION; GENE EXPRESSION PROFILING; MICRORNAS; ORGAN SPECIFICITY; RNA STABILITY; TRANSCRIPTOME;

EID: 84919402715     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-014-3530-x     Document Type: Article

References (32)

1. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
2. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843–854
3. Bustin SA, Benes V, Nolan T, Pfaffl MW (2005) Quantitative real time RT-PCR—a perspective. J Mol Endocrinol 34:597–601
4. Bustin SA, Nolan T (2004) Pitfalls of quantitative real-time reverse transcription polymerase chain reaction. J Biomol Tech 15(3):155–166
5. Li GL, Roy B, Li XH, Yue WF, Wu XF, Liu JM, Zhang CX, Miao YG (2009) Quantification of silkworm coactivator of MBF1 mRNA by SYBR Green I real-time RT-PCR reveals tissue- and stage-specific transcription levels. Mol Biol Rep 36:1217–1223
6. Tricarico C, Pinzani P, Bianchi S, Paglierani M, Distante V, Pazzagli M, Bustin SA, Orlando C (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(2):293–300
7. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3(7):34. doi:10.1186/gb-2007-3-8-research0034
8. Lee PD, Sladek R, Greenwood CM, Hudson TJ (2002) Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res 12(2):292–297
9. Yang YF, Hou S, Cui GH, Chen SL, Wei JH, Huang LQ (2010) Characterization of reference genes for quantitative real-time PCR analysis in various tissues of Salvia miltiorrhiza. Mol Biol Rep 37:507–513
10. Jiang HB, Liu YH, Tang PA, Zhou AW, Wang JJ (2010) Validation of endogenous reference genes for insecticide-induced and developmental expression profiling of Liposcelis bostsrychophila (Psocoptera: Liposcelididae). Mol Biol Rep 37:1019–1029
11. de Jacques B, Kok RW, Roelofs BA, Giesendorf JL, Pennings ET, Waas TF, Swinkels DW, Span PN (2005) Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Investig 85:154–159. doi:10.1038/labinvest.3700208
12. Nygard A-B, Jørgensen CB, Cirera S, Fredholm M (2007) Selection of reference genes for gene expression studies in pig tissues using SYBR Green qPCR. BMC Mol Biol 8:67. doi:10.1186/1471-2199-8-67
13. Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A (2004) Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun 313:856–862. doi:10.1016/j.bbrc.2003.11.177
14. Bas A, Forsberg G, Hammarstrom S, Hammarstrom M-L (2004) Utility of the housekeeping Genes 18S rRNA, b-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 59:566–573
15. Kiss T (2002) Small nucleolar RNAs: an abundant group of non-coding RNAs with diverse cellular functions. Cell 109:145–148
16. ® microRNA assays. Appl Biosyst Appl Note 127AP11–01:1–8
17. Mortarino M, Gioia G, Gelain ME, Albonico F, Roccabianca P, Ferri E, Comazzi S (2010) Identification of suitable endogenous controls and differentially expressed microRNAs in canine fresh-frozen and FFPE lymphoma samples. Leuk Res 34(8):1070–1077
18. Peltier HJ, Latham GJ (2008) Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues. RNA 14:844–852
19. Davoren PA, McNeill RE, Lowery AJ, Kerin MJ, Miller N (2008) Identification of suitable endogenous control genes for microRNA gene expression analysis in human breast cancer. BMC Mol Biol 9:76–87. doi:10.1186/1471-2199-9-76
20. Chang KH, Mestdagh P, Vandesompele J, Kerin MJ, Miller N (2010) MicroRNA expression profiling to identify and validate reference genes for relative quantification in colorectal cancer. BMC Cancer 10:173–186
21. Liang Y, Ridzon D, Wong L, Chen C (2007) Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 8:166. doi:10.1186/1471-2164-8-166
22. Andersen CL, Jensen JL, Orntoft TF (2004) 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 64:5245–5250
23. Silver N, Best S, Jiang J, Thein SL (2006) Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time. PCR BMC Mol Biol 7:33
24. Brunner AM, Yakovlev IA, Strauss SH (2004) Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol 4:14
25. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP (2004) Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pairwise correlations. Biotechnol Lett 26:509–515
26. Jin W, Grant JR, Stothard P, Moore SS, Guan LL (2009) Characterization of bovine miRNAs by sequencing and bioinformatics analysis. BMC Mol Biol 10:90. doi:10.1186/1471-2199-10-90
27. Timoneda O, Balcells I, Cordoba S, Castello A, Sánchez A (2012) Determination of reference microRNAs for relative quantification in porcine tissues. PLoS ONE 7(9):e44413. doi:10.1371/journal.pone.0044413
28. Hossain MM, Ghanem N, Hoelker M, Rings F, Phatsara C, Tholen E, Schellander K, Tesfaye D (2009) Identification and characterization of miRNAs expressed in the bovine ovary. BMC Genomics 10:443. doi:10.1186/1471-2164-10-443
29. Pfaffl MW (2004) Quantification strategies in real-time PCR. In: Bustin SA (ed) A-Z of quantitative PCR. IUL Biotechnology Series, International University Line, La Jolla, CA, pp 87–120
30. Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, Endoh H, Harano T, Yatabe Y, Nagino M, Nimura Y, Mitsudomi T, Takahashi T (2004) Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 64(11):3753–3756
31. Pineles BL, Romero R, Montenegro D, Tarca AL, Han YM, Kim YM, Draghici S, Espinoza J, Kusanovic JP, Mittal P, Hassan SS, Kim CJ (2007) Distinct subsets of microRNAs are expressed differentially in the human placentas of patients with preeclampsia. Am J Obstet Gynecol 196(3):261 e1-6
32. Goossens K, Van Poucke M, Van Soom A, Vandesompele J, Van Zeveren A, Peelman LJ (2005) Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos. BMC Dev Biol 5:27–36