Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs

RNA

Volumn 11, Issue 11, 2005, Pages 1737-1744

  Raymond, Christopher K ^a   Roberts, Brian S ^a   Garrett Engele, Phillip ^a   Lim, Lee P ^a   Johnson, Jason M ^a  

^a ROSETTA INPHARMATICS   (United States)

Author keywords

Locked nucleic acid; microRNA; Primer extension; Quantitative PCR; siRNA; SYBR green

Indexed keywords

COMPLEMENTARY DNA; MICRORNA; SMALL INTERFERING RNA;

ANALYTIC METHOD; ARTICLE; GENE SEQUENCE; MOLECULAR DYNAMICS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION; SENSITIVITY AND SPECIFICITY;

DNA PRIMERS; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; HUMANS; MICRORNAS; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION; RNA, SMALL INTERFERING; TISSUE DISTRIBUTION;

EID: 27144543663     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2148705     Document Type: Article

References (23)

1. Allawi, H.T., Dahlberg, J.E., Olson, S., Lund, E., Olson, M., Ma, W.P., Takova, T., Neri, B.P., and Lyamichev, V.I. 2004. Quantitation of microRNAs using a modified Invader assay. RNA 10: 1153-1161.
2. Babak, T., Zhang, W., Morris, Q., Blencowe, B.J., and Hughes, T.R. 2004. Probing microRNAs with microarrays: Tissue specificity and functional inference. RNA 10: 1813-1819.
3. Barad, O., Meiri, E., Avniel, A., Aharonov, R., Barzilai, A., Bentwich, I., Einav, U., Gilad, S., Hurban, P., Karov, Y., et al. 2004. MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues. Genome Res. 14: 2486-2494.
4. Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
5. Baskerville, S. and Bartel, D.P. 2005. Microarray profiling of micro-RNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241-247.
6. Hartig, J.S., Grune, I., Najafi-Shoushtari, S.H., and Famulok, M. 2004. Sequence-specific detection of MicroRNAs by signal-amplifying ribozymes. J. Am. Chem. Soc. 126: 722-723.
7. Lagos-Quintana, M., Rauhut, R., Meyer, J., Borkhardt, A., and Tuschl, T. 2003. New microRNAs from mouse and human. RNA 9: 175-179.
8. Lim, L.P., Lau, N.C., Garrett-Engele, P., Grimson, A., Schelter, J.M., Castle, J., Bartel, D.P., Linsley, P.S., and Johnson, J.M. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
9. Liu, J., Carmell, M.A., Rivas, F.V., Marsden, C.G., Thomson, J.M., Song, J.J., Hammond, S.M., Joshua-Tor, L., and Hannon, G.J. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441.
10. Matzke, M.A. and Birchler, J.A. 2005. RNAi-mediated pathways in the nucleus. Nat. Rev. Genet. 6: 24-35.
11. Miska, E.A., Alvarez-Saavedra, E., Townsend, M., Yoshii, A., Sestan, N., Rakic, P., Constantine-Paton, M., and Horvitz, H.R. 2004. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 5: R68.
12. Morris, K.V., Chan, S.W., Jacobsen, S.E., and Looney, D.J. 2004. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305: 1289-1292.
13. Nelson, P.T., Baldwin, D.A., Scearce, L.M., Oberholtzer, J.C., Tobias, J.W., and Mourelatos, Z. 2004. Microarray-based, high-throughput gene expression profiling of microRNAs. Nat. Methods 1: 155-161.
14. Petersen, M. and Wengel, J. 2003. LNA: A versatile tool for therapeutics and genomics. Trends Biotechnol. 21: 74-81.
15. Raymond, C.K., Castle, J., Garrett-Engele, P., Armour, C.D., Kan, Z., Tsinoremas, N., and Johnson, J.M. 2004. Expression of alternatively spliced sodium channel α-subunit genes. Unique splicing patterns are observed in dorsal root ganglia. J. Biol. Chem. 279: 46234-46241.
16. Schmittgen, T.D., Jiang, J., Liu, Q., and Yang, L. 2004. A highthroughput method to monitor the expression of microRNA precursors. Nucleic Acids Res. 32: e43.
17. Sempere, L.F., Freemantle, S., Pitha-Rowe, I., Moss, E., Dmitrovsky, E., and 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 Biol. 5: R13.
18. Song, J.J., Smith, S.K., Hannon, G.J., and Joshua-Tor, L. 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305: 1434-1437.
19. Sun, Y., Koo, S., White, N., Peralta, E., Esau, C., Dean, N.M., and Perera, R.J. 2004. Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucleic Acids Res. 32: e188.
20. Tang, G. 2005. siRNA and miRNA: An insight into RISCs. Trends Biochem. Sci. 30: 106-114.
21. Thomson, J.M., Parker, J., Perou, C.M., and Hammond, S.M. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53.
22. Tomari, Y. and Zamore, P.D. 2005. Perspective: Machines for RNAi. Genes & Dev. 19: 517-529.
23. Zeng, Y. and Cullen, B.R. 2003. Sequence requirements for micro RNA processing and function in human cells. RNA 9: 112-123.