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

Volumn 9, Issue , 2008, Pages

  Sharbati Tehrani, Soroush ^a   Kutz Lohroff, Barbara ^a   Bergbauer, Ramona ^a   Scholven, Jutta ^a   Einspanier, Ralf ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

FLUOROCHROME; LOCKED NUCLEIC ACID; MICRORNA; OLIGONUCLEOTIDE; LET 7 MICRORNA, HUMAN; LET-7 MICRORNA, HUMAN;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; HUMAN; HUMAN CELL; INTESTINE; NONHUMAN; NUCLEIC ACID ANALYSIS; QUANTITATIVE ASSAY; QUANTITATIVE GENETICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; ANIMAL; CELL STRAIN HT29; DNA DENATURATION; GENE EXPRESSION REGULATION; GENETICS; HELA CELL; METABOLISM; METHODOLOGY; REPRODUCIBILITY; SWINE;

EUKARYOTA; SUS;

ANIMALS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HELA CELLS; HT29 CELLS; HUMANS; INTESTINES; MICRORNAS; NUCLEIC ACID DENATURATION; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SWINE;

EID: 44349101865     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-9-34     Document Type: Article

References (30)

1. Kloosterman WP Plasterk RH The diverse functions of microRNAs in animal development and disease Dev Cell 2006, 11:441-450. 10.1016/ j.devcel.2006.09.009 17011485
2. Hamilton AJ Baulcombe DC A species of small antisense RNA in posttranscriptional gene silencing in plants Science 1999, 286:950-952. 10.1126/science.286.5441.950 10542148
3. Zhang B Wang Q Pan X MicroRNAs and their regulatory roles in animals and plants J Cell Physiol 2007, 210:279-289. 10.1002/jcp.20869 17096367
4. Kim VN Nam JW Genomics of microRNA Trends Genet 2006, 22:165-173. 10.1016/j.tig.2006.01.003 16446010
5. Jackson RJ Standart N How do microRNAs regulate gene expression? Sci STKE 2007, 2007:rE1. 10.1126/stke.3672007re1 17200520
6. Kim J Krichevsky A Grad Y Hayes GD Kosik KS Church GM Ruvkun G Identification of many microRNAs that copurify with polyribosomes in mammalian neurons Proc Natl Acad Sci U S A 2004, 101:360-365. 314190 14691248 10.1073/pnas.2333854100
7. Lee RC Ambros V An extensive class of small RNAs in Caenorhabditis elegans Science 2001, 294:862-864. 10.1126/science.1065329 11679672
8. Babak T Zhang W Morris Q Blencowe BJ Hughes TR Probing microRNAs with microarrays: Tissue specificity and functional inference Rna 2004, 10:1813-1819. 1370668 15496526 10.1261/rna.7119904
9. Nelson PT Baldwin DA Scearce LM Oberholtzer JC Tobias JW Mourelatos Z Microarray-based, high-throughput gene expression profiling of microRNAs Nat Methods 2004, 1:155-161. 10.1038/nmeth717 15782179
10. Liang RQ Li W Li Y Tan CY Li JX Jin YX Ruan KC An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe Nucleic Acids Res 2005, 33:e17. 548377 15684409 10.1093/nar/gni019
11. Neely LA Patel S Garver J Gallo M Hackett M McLaughlin S Nadel M Harris J Gullans S Rooke J A single-molecule method for the quantitation of microRNA gene expression Nat Methods 2006, 3:41-46. 10.1038/nmeth825 16369552
12. Wong ML Medrano JF Real-time PCR for mRNA quantitation Biotechniques 2005, 39:75-85. 16060372
13. Malinen E Kassinen A Rinttila T Palva A Comparison of real-time PCR with SYBR Green I or 5′-nuclease assays and dot-blot hybridization with rDNA-targeted oligonucleotide probes in quantification of selected faecal bacteria Microbiology 2003, 149:269-277. 10.1099/mic.0.25975-0 12576600
14. Palmer S Wiegand AP Maldarelli F Bazmi H Mican JM Polis M Dewar RL Planta A Liu S Metcalf JA Mellors JW Coffin JM New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus type 1 RNA in plasma J Clin Microbiol 2003, 41:4531-4536. 254331 14532178 10.1128/JCM.41.10.4531-4536.2003
15. Schmittgen TD Jiang J Liu Q Yang L A high-throughput method to monitor the expression of microRNA precursors Nucleic Acids Res 2004, 32:e43. 390315 14985473 10.1093/nar/gnh040
16. Jiang J Lee EJ Gusev Y Schmittgen TD Real-time expression profiling of microRNA precursors in human cancer cell lines Nucleic Acids Res 2005, 33:5394-5403. 1236977 16192569 10.1093/nar/gki863
17. Lagos-Quintana M Rauhut R Yalcin A Meyer J Lendeckel W Tuschl T Identification of tissue-specific microRNAs from mouse Curr Biol 2002, 12:735-739. 10.1016/S0960-9822(02)00809-6 12007417
18. Raymond CK Roberts BS Garrett-Engele P Lim LP Johnson JM Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs Rna 2005, 11:1737-1744. 1370860 16244135 10.1261/rna.2148705
19. 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 Real-time quantification of microRNAs by stem-loop RT-PCR Nucleic Acids Res 2005, 33:e179. 1292995 16314309 10.1093/nar/gni178
20. Griffiths-Jones S Grocock RJ van Dongen S Bateman A Enright AJ miRBase: microRNA sequences, targets and gene nomenclature Nucleic Acids Res 2006, 34:D140-4. 1347474 16381832 10.1093/nar/gkj112
21. 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. RESEARCH0034 126239 12184808 10.1186/gb-2002-3-7-research0034
22. Lewis BP Burge CB Bartel DP Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets Cell 2005, 120:15-20. 10.1016/j.cell.2004.12.035 15652477
23. Alvarez-Garcia I Miska EA MicroRNA functions in animal development and human disease Development 2005, 132:4653-4662. 10.1242/dev.02073 16224045
24. Chan JA Krichevsky AM Kosik KS MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells Cancer Res 2005, 65:6029-6033. 10.1158/ 0008-5472.CAN-05-0137 16024602
25. Si ML Zhu S Wu H Lu Z Wu F Mo YY miR-21-mediated tumor growth Oncogene 2007, 26:2799-2803. 10.1038/sj.onc.1210083 17072344
26. Michael MZ SM OC van Holst Pellekaan NG Young GP James RJ Reduced accumulation of specific microRNAs in colorectal neoplasia Mol Cancer Res 2003, 1:882-891. 14573789
27. Iorio MV Ferracin M Liu CG Veronese A Spizzo R Sabbioni S Magri E Pedriali M Fabbri M Campiglio M Menard S Palazzo JP Rosenberg A Musiani P Volinia S Nenci I Calin GA Querzoli P Negrini M Croce CM MicroRNA gene expression deregulation in human breast cancer Cancer Res 2005, 65:7065-7070. 10.1158/0008-5472.CAN-05-1783 16103053
28. Mocellin S Rossi CR Pilati P Nitti D Marincola FM Quantitative real-time PCR: A powerful ally in cancer research Trends Mol Med 2003, 9:189-195. 10.1016/S1471-4914(03)00047-9 12763523
29. Volinia S Calin GA Liu CG Ambs S Cimmino A Petrocca F Visone R Iorio M Roldo C Ferracin M Prueitt RL Yanaihara N Lanza G Scarpa A Vecchione A Negrini M Harris CC Croce CM A microRNA expression signature of human solid tumors defines cancer gene targets Proc Natl Acad Sci U S A 2006, 103:2257-2261. 1413718 16461460 10.1073/pnas.0510565103
30. Bandres E Cubedo E Agirre X Malumbres R Zarate R Ramirez N Abajo A Navarro A Moreno I Monzo M Garcia-Foncillas J Identification by Real-time PCR of 13 mature microRNAs differentially expressed in colorectal cancer and non-tumoral tissues Mol Cancer 2006, 5:29. 1550420 16854228 10.1186/1476-4598-5-29