Identification of suitable endogenous control microRNA genes in normal pig tissues

Animal Science Journal

Volumn 82, Issue 6, 2011, Pages 722-728

  Gu, Yiren ^a,b   Li, Mingzhou ^a   Zhang, Kai ^a   Chen, Lei ^c   Jiang, An an ^a   Wang, Jinyong ^c   Lv, Xuebin ^b   Li, Xuewei ^a  

^a SICHUAN AGRICULTURAL UNIVERSITY   (China)

^b SICHUAN ANIMAL SCIENCE ACADEMY   (China)

^c Chongqing Academy of Animal Sciences   (China)

Author keywords

Endogenous control gene; MiRNA; Normalization; Pig; Quantitative real time PCR

Indexed keywords

MICRORNA;

ADIPOSE TISSUE; ANIMAL; ARTICLE; FEMALE; GENE EXPRESSION REGULATION; GENETICS; MALE; METHODOLOGY; MUSCLE; POLYMERASE CHAIN REACTION; SWINE;

ADIPOSE TISSUE; ANIMALS; FEMALE; GENE EXPRESSION REGULATION; MALE; MICRORNAS; MUSCLES; POLYMERASE CHAIN REACTION; SUS SCROFA;

SUIDAE; SUS;

EID: 82255162879     PISSN: 13443941     EISSN: 17400929     Source Type: Journal    
DOI: 10.1111/j.1740-0929.2011.00908.x     Document Type: Article

References (28)

1. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
2. Beuvink I, Kolb FA, Budach W, Garnier A, Lange J, Natt F, Dengler U, Hall J, Filipowicz W, Weiler J. 2007. A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs. Nucleic Acids Research 35, e52. doi:10.1093/nar/gkl1118.
3. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ. 2005. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research 33, e179. doi:10.1093/nar/gni178.
4. Corney DC, Flesken-Nikitin A, Godwin AK, Wang W, Nikitin AY. 2007. MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth. Cancer Research 67, 8433-8438.
5. 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 Molecular Biology 9, 76. doi:10.1186/1471-2199-9-76.
6. de Kok JB, Roelofs RW, Giesendorf BA, Pennings JL, Waas ET, Feuth T, Swinkels DW, Span PN. 2005. Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Laboratory Investigation 85, 154-159.
7. Feng J, Wang K, Liu X, Chen S, Chen J. 2009. The quantification of tomato microRNAs response to viral infection by stem-loop real-time RT-PCR. Gene 437, 14-21.
8. Huggett J, Dheda K, Bustin S, Zumla A. 2005. Real-time RT-PCR normalisation; strategies and considerations. Genes and Immunity 6, 279-284.
9. Kim J, Cho IS, Hong JS, Choi YK, Kim H, Lee YS. 2008. Identification and characterization of new microRNAs from pig. Mammalian Genome 19, 570-580.
10. Kloosterman WP, Plasterk RH. 2006. The diverse functions of microRNAs in animal development and disease. Developmental Cell 11, 441-450.
11. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294, 853-858.
12. Lau NC, Lim LP, Weinstein EG, Bartel DP. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-862.
13. 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.
14. Livak K, Schmittgen T. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2-[Delta][Delta] CT method. Methods 25, 402-408.
15. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR. 2005. MicroRNA expression profiles classify human cancers. Nature 435, 834-838.
16. Mao F, Leung WY, Xin X. 2007. Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications. BMC Biotechnology 7, 76. doi:10.1186/1472-6750-7-76.
17. Mattie MD, Benz CC, Bowers J, Sensinger K, Wong L, Scott GK, Fedele V, Ginzinger D, Getts R, Haqq C. 2006. Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Molecular Cancer 5, 24. doi:10.1186/1476-4598-5-24.
18. Mestdagh P, Van Vlierberghe P, De Weer A, Muth D, Westermann F, Speleman F, Vandesompele J. 2009. A novel and universal method for microRNA RT-qPCR data normalization. Genome Biology 10, R64. doi:10.1186/gb-2009-10-6-r64.
19. Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P, Constantine-Paton M, Horvitz HR. 2004. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biology 5, R68. doi:10.1186/gb-2004-5-9-r68.
20. Nelson PT, Baldwin DA, Scearce LM, Oberholtzer JC, Tobias JW, Mourelatos Z. 2004. Microarray-based, high-throughput gene expression profiling of microRNAs. Nature Methods 1, 155-161.
21. 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.
22. Pradervand S, Weber J, Thomas J, Bueno M, Wirapati P, Lefort K, Dotto GP, Harshman K. 2009. Impact of normalization on miRNA microarray expression profiling. RNA 15, 493-501.
23. Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V. 2004. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biology 5, R13.
24. Sharbati-Tehrani S, Kutz-Lohroff B, Bergbauer R, Scholven J, Einspanier R. 2008a. miR-Q: a novel quantitative RT-PCR approach for the expression profiling of small RNA molecules such as miRNAs in a complex sample. BMC Molecular Biology 9, 34. doi:10.1186/1471-2199-9-34.
25. Sharbati-Tehrani S, Kutz-Lohroff B, Scholven J, Einspanier R. 2008b. Concatameric cloning of porcine microRNA molecules after assembly PCR. Biochemical and Biophysical Research Communications 375, 484-489.
26. Stahlberg A, Hakansson J, Xian X, Semb H, Kubista M. 2004. Properties of the reverse transcription reaction in mRNA quantification. Clinical Chemistry 50, 509-515.
27. 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 Biology 3, RESEARCH0034. doi:10.1186/gb-2002-3-7-research0034.
28. Xie SS, Huang TH, Shen Y, Li XY, Zhang XX, Zhu MJ, Qin HY, Zhao SH. 2010. Identification and characterization of microRNAs from porcine skeletal muscle. Animal Genetics 41, 179-190.