Detection and quantitation of microRNAs using the RNA Invader<span class='sup'>®</span> assay

doi:10.1017/CBO9780511541766.021

18 - Detection and quantitation of microRNAs using the RNA Invader® assay

from IV - Detection and quantitation of microRNAs

Published online by Cambridge University Press: 22 August 2009

Hatim T. Allawi and

Victor I. Lyamichev

Edited by

Krishnarao Appasani

Foreword by

Sidney Altman and

Victor R. Ambros

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Hatim T. Allawi: Affiliation:
Third Wave Technologies, Inc. 502 S. Rosa Rd Madison, WI 53719-1256 USA
Victor I. Lyamichev: Affiliation:
Third Wave Technologies, Inc. 502 S. Rosa Rd Madison, WI 53719-1256 USA

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Summary

Introduction

MicroRNAs are short single-stranded RNA molecules ranging in length from 17 to 24 nucleotides. During the past few years, hundreds of miRNAs have been identified in plants, animals, and a number of viruses with their exact biological function not fully understood (Lagos-Quintana et al., 2001; Lagos-Quintana et al., 2002; Reinhart et al., 2002; Hunter and Poethig, 2003; Lagos-Quintana et al., 2003; Pfeffer et al., 2004; Dunn et al., 2005; Pasquinelli et al., 2005; Wienholds and Plasterk, 2005; Wienholds et al., 2005). It has been shown that miRNAs target messenger RNA (mRNAs) at specific sites inducing cleavage of the RNA or result in inhibition of translation (Bartel, 2004). MiRNAs also exhibit unique expression patterns in tumor cells and therefore maybe useful as molecular markers for cancer cells (Michael et al., 2003; Calin et al., 2004; Croce and Calin, 2005; Eis et al., 2005). Moreover, microRNAs have been identified to be involved in regulation of cell and tissue development as well as several biological processes including cell proliferation and death, apoptosis, neuron development, DNA methylation and chromatin modification, and fat metabolism (Reinhart et al., 2000; Pasquinelli and Ruvkun, 2002; Ambros, 2003; Brennecke et al., 2003; Johnston and Hobert, 2003; Xu et al., 2003; Bao et al., 2004; Alvarez-Garcia and Miska, 2005; Croce and Calin, 2005; Miska, 2005).

Several methods of detecting and quantitating miRNAs have been developed. The size and sequence homology of some miRNAs makes their quantitation and differentiation challenging to conventional RT-PCR methods or standard microchip hybridization techniques.

Type: Chapter
Information: MicroRNAs
From Basic Science to Disease Biology
, pp. 242 - 254

DOI: https://doi.org/10.1017/CBO9780511541766.021 [Opens in a new window]

Publisher: Cambridge University Press

Print publication year: 2007

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References

Allawi, H. T. and SantaLucia, J. Jr. (1997). Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry, 36, 10581–10594.Google Scholar

Allawi, H. T. and SantaLucia, J. Jr. (1998). Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. Biochemistry, 37, 9435–9444.Google Scholar

Allawi, H. T., Dahlberg, J. E., Olson, S.et al. (2004). Quantitation of microRNAs using a modified Invader assay. RNA, 10, 1153–1161.Google Scholar

Alvarez-Garcia, I. and Miska, E. A. (2005). MicroRNA functions in animal development and human disease. Development, 132, 4653–4662.Google Scholar

Ambros, V. (2003). MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell, 113, 673–676.Google Scholar

Bao, N., Lye, K. W. and Barton, M. K. (2004). MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Developmental Cell, 7, 653–662.Google Scholar

Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281–297.Google Scholar

Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B. and Cohen, S. M. (2003). bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell, 113, 25–36.Google Scholar

Burczynski, M. E., McMillian, M., Parker, J. B.et al. (2001). Cytochrome P450 induction in rat hepatocytes assessed by quantitative real-time reverse-transcription polymerase chain reaction and the RNA invasive cleavage assay. Drug Metabolism Disposition, 29, 1243–1250.Google Scholar

Busten, S. A. (2002). Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. Journal of Molecular Endocrinology, 29, 23–29.Google Scholar

Calin, G. A., Sevignani, C., Dumitru, C. D.et al. (2004). Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proceedings of the National Academy of Sciences USA, 101, 2999–3004.Google Scholar

Cantor, C. R., Warshaw, M. M. and Shapiro, H. (1970). Biopolymers, 9, 1059–1077.

Chen, C., Ridzon, D. A., Broomer, A. J.et al. (2005). Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research, 33, e179.Google Scholar

Croce, C. M. and Calin, G. A. (2005). miRNAs, cancer, and stem cell division. Cell, 122, 6–7.Google Scholar

Arruda, M., Lyamichev, V. I., Eis, P. S.et al. (2002). Invader technology for DNA and RNA analysis: principles and applications. Expert Reviews in Molecular Diagnostics, 2, 487–496.Google Scholar

Dunn, W., Trang, P., Zhong, Q.et al. (2005). Human cytomegalovirus expresses novel microRNAs during productive viral infection. Cell Microbiology, 7, 1684–1695.Google Scholar

Eis, P. S., Olson, M. C., Takova, T.et al. (2001). An invasive cleavage assay for direct quantitation of specific RNAs. Nature Biotechnology, 19, 673–676.Google Scholar

Eis, P. S., Tam, W., Sun, L.et al. (2005). Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proceedings of the National Academy of Sciences USA, 102, 3627–3632.Google Scholar

Hall, J. G., Eis, P. S., Law, S. M.et al. (2000). Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proceedings of the National Academy of Sciences USA 97, 8272–8277.Google Scholar

Hunter, C. and Poethig, R. S. (2003). miSSING LINKS: miRNAs and plant development. Current Opinion in Genetics & Development, 13, 372–378.Google Scholar

Johnston, R. J. and Hobert, O. (2003). A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature, 426, 845–849.Google Scholar

Kaiser, M. W., Lyamicheva, N., Ma, W.et al. (1999). A comparison of eubacterial and archaeal structure-specific 5′-exonucleases. Journal of Biological Chemistry, 274, 21 387–21 394.Google Scholar

Krichevsky, A. M., King, K. S., Donahue, C. P., Khrapko, K. and Kosik, K. S. (2003). A microRNA array reveals extensive regulation of microRNAs during brain development. RNA, 9, 1274–1281.Google Scholar

Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. Science, 294, 853–858.Google Scholar

Lagos-Quintana, M., Rauhut, R., Yalcin, A.et al. (2002). Identification of tissue-specific microRNAs from mouse. Current Biology, 12, 735–739.Google Scholar

Lagos-Quintana, M., Rauhut, R., Meyer, J., Borkhardt, A. and Tuschl, T. (2003). New microRNAs from mouse and human. RNA, 9, 175–179.Google Scholar

Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B. and Bartel, D. P. (2003). Vertebrate microRNA genes. Science, 299, 1540.Google Scholar

Liu, C. G., Calin, G. A., Meloon, B.et al. (2004). An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proceedings of the National Academy of Sciences USA, 101, 9740–9744.Google Scholar

Lyamichev, V., Mast, A. L., Hall, J. G.et al. (1999). Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nature Biotechnology, 17, 292–296.Google Scholar

Lyamichev, V. I., Kaiser, M. W., Lyamicheva, N. E.et al. (2000). Experimental and theoretical analysis of the invasive signal amplification reaction. Biochemistry, 39, 9523–9532.Google Scholar

Michael, M. Z., O'Connor, S. M., Holst Pellekaan, N. G., Young, G. P. and James, R. J. (2003). Reduced accumulation of specific microRNAs in colorectal neoplasia. Molecular Cancer Research, 1, 882–891.Google Scholar

Mills, J. B., Rose, K. A., Sadagopan, N., Sahi, J. and Morais, S. M. (2004). Induction of drug metabolism enzymes and MDR1 using a novel human hepatocyte cell line. Journal of Pharmacology and Experimental Therapy, 309, 303–309.Google Scholar

Miska, E. A. (2005). How microRNAs control cell division, differentiation and death. Current Opinion in Genetics & Development, 15, 563–568.Google Scholar

Pasquinelli, A. E. and Ruvkun, G. (2002). Control of developmental timing by microRNAs and their targets. Annual Reviews of Cell Developmental Biology, 18, 495–513.Google Scholar

Pasquinelli, A. E., Hunter, S. and Bracht, J. (2005). MicroRNAs: a developing story. Current Opinion in Genetics & Development, 15, 200–205.Google Scholar

Pfeffer, S., Zavolan, M., Grasser, F. A.et al. (2004). Identification of virus-encoded microRNAs. Science, 304, 734–736.Google Scholar

Reinhart, B. J., Slack, F. J., Basson, M.et al. (2000). The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403, 901–906.Google Scholar

Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B. and Bartel, D. P. (2002). MicroRNAs in plants. Genes & Development, 16, 1616–1626.Google Scholar

Wagner, E. J., Curtis, M. L., Robson, N. D.et al. (2003). Quantification of alternatively spliced FGFR2 RNAs using the RNA invasive cleavage assay. RNA, 9, 1552–1561.Google Scholar

Walter, A. E. and Turner, D. H. (1994). Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry, 33, 12715–12719.Google Scholar

Walter, A. E., Turner, D. H., Kim, J.et al. (1994). Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proceedings of the National Academy of Sciences USA, 91, 9218–9222.Google Scholar

Wienholds, E. and Plasterk, R. H. (2005). MicroRNA function in animal development, Federation of the European Biochemical Society Letters, 579, 5911–5922.Google Scholar

Wienholds, E., Kloosterman, W. P., Miska, E.et al. (2005). MicroRNA expression in zebrafish embryonic development. Science, 309, 310–311.Google Scholar

Xu, P., Vernooy, S. Y., Guo, M. and Hay, B. A. (2003). The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Current Biology, 13, 790–795.Google Scholar

Zeng, Y. and Cullen, B. R. (2003). Sequence requirements for micro RNA processing and function in human cells. RNA, 9, 112–123.Google Scholar