Quantitation of microRNAs using a modified Invader assay

RNA

Volumn 10, Issue 7, 2004, Pages 1153-1161

  Allawi, Hatim T ^a   Dahlberg, James E ^b   Olson, Sarah ^a   Lund, Elsebet ^b   Olson, Marilyn ^a   Ma, Wu Po ^a   Takova, Tsetska ^a   Neri, Bruce P ^a   Lyamichev, Victor I ^a  

^a Third Wave Technologies Inc   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

2 O methyl; Cell lysates; Invader assay; MiRNA; RNAi; SiRNA; Structure specific 5 nuclease

Indexed keywords

DETERGENT; MESSENGER RNA; MICRORNA; NUCLEOTIDE; RNA PRECURSOR;

ARTICLE; ASSAY; CELL LYSATE; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA ANALYSIS; SENSITIVITY ANALYSIS;

BASE SEQUENCE; CELL LINE; GENETIC TECHNIQUES; HELA CELLS; HUMANS; MICRORNAS; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES;

EID: 3042663131     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5250604     Document Type: Article

References (29)

1. Banerjee, D. and Slack, F. 2002. Control of developmental timing by small temporal RNAs: A paradigm for RNA-mediated regulation of gene expression. Bioessays 24: 119-129.
2. Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
3. Bevington, P.R. 1969. Propagation of errors. In Data reduction and error analysis for the physical sciences, pp. 56-60. McGraw-Hill Book Company, New York.
4. Cantor, C.R., Warshaw, M.M., and Shapiro, H. 1970. Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers 9: 1059-1077.
5. Carmell, M.A., Xuan, Z., Zhang, M.Q., and Hannon, G.J. 2002. The Argonaute family: Tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes & Dev. 16: 2733-2742.
6. Carrington, J.C. and Ambros, V. 2003. Role of microRNAs in plant and animal development. Science 301: 336-338.
7. de Arruda, M., Lyamichev, V.I., Eis, P.S., Iszczyszyn, W., Kwiatkowski, R.W., Law, S.M., Olson, M.C., and Rasmussen, E.B. 2002. Invader technology for DNA and RNA analysis: Principles and applications. Expert Rev. Mol. Diagn. 2: 487-496.
8. Dykxhoorn, D.M., Novina, C.D., and Sharp, P.A. 2003. Killing the messenger: Short RNAs that silence gene expression. Nat. Rev. Mol. Cell. Biol. 4: 457-467.
9. Eis, P.S., Olson, M.C., Takova, T., Curtis, M.L., Olson, S.M., Vener, T.I., Ip, H.S., Vedvik, K.L., Bartholomay, C.T., Allawi, H.T., et al. 2001. An invasive cleavage assay for direct quantitation of specific RNAs. Nat. Biotechnol. 19: 673-676.
10. Hall, J.G., Eis, P.S., Law, S.M., Reynaldo, L.P., Prudent, J.R., Marshall, D.J., Allawi, H.T., Mast, A.L., Dahlberg, J.E., Kwiatkowski, R.W., et al. 2000. Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc. Natl. Acad. Sci. 97: 8272-8277.
11. Kaiser, M.W., Lyamicheva, N., Ma, W., Miller, C., Neri, B., Fors, L., and Lyamichev, V.I. 1999. A comparison of eubacterial and archaeal structure-specific 5′-exonucleases. J. Biol. Chem. 274: 21387-21394.
12. Kidner, C.A. and Martienssen, R.A. 2003. Macro effects of microRNAs in plants. Trends Genet. 19: 13-16.
13. Kim, J., Krichevsky, A., Grad, Y., Hayes, G.D., Kosik, K.S., Church, G.M., and Ruvkun, G. 2004. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl. Acad. Sci. 101: 360-365.
14. 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.
15. Lagos-Quintana, M., Rauhut, R., Lendeckel, W., and Tuschl, T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
16. Lau, N.C., Lim, L.P., Weinstein, E.G., and Bartel, D.P. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.
17. Lee, R.C. and Ambros, V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864.
18. Lee, R.C., Feinbaum, R.L., and Ambros, V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
19. Lim, L.P., Lau, N.C., Weinstein, E.G., Abdelhakim, A., Yekta, S., Rhoades, M.W., Burge, C.B., and Bartel, D.P. 2003. The microRNAs of Caenorhabditis elegans. Genes & Dev. 17: 991-1008.
20. Lund, E., Guttinger, S., Calado, A., Dahlberg, J.E., and Kutay, U. 2003. Nuclear export of microRNA precursors. Science. 303: 95-98.
21. Lyamichev, V., Mast, A.L., Hall, J.G., Prudent, J.R., Kaiser, M.W., Takova, T., Kwiatkowski, R.W., Sander, T.J., de Arruda, M., Arco, D.A., et al. 1999. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol. 17: 292-296.
22. Lyamichev, V.I., Kaiser, M.W., Lyamicheva, N.E., Vologodskii, A.V., Hall, J.G., Ma, W.P., Allawi, H.T., and Neri, B.P. 2000. Experimental and theoretical analysis of the invasive signal amplification reaction. Biochemistry 39: 9523-9532.
23. Moss, E.G. and Poethig, R.S. 2002. MicroRNAs: Something new under the sun. Curr. Biol. 12: R688-R690.
24. Mourelatos, Z., Dostie, J., Paushkin, S., Sharma, A., Charroux, B., Abel, L., Rappsilber, J., Mann, M., and Dreyfuss, G. 2002. miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs. Genes & Dev. 16: 720-728.
25. Pasquinelli, A.E. and Ruvkun, G. 2002. Control of developmental timing by micrornas and their targets. Annu. Rev. Cell. Dev. Biol. 18: 495-513.
26. Pasquinelli, A.E., Reinhart, B.J., Slack, F., Martindale, M.Q., Kuroda, M.I., Maller, B., Hayward, D.C., Ball, E.E., Degnan, B., Muller, P., et al. 2000. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 86-89.
27. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P. 2002. MicroRNAs in plants. Genes & Dev. 16: 1616-1626.
28. Sempere, L.S., 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.
29. Wagner, E.J., Curtis, M.L., Robson, N.D., Baraniak, A.P., Eis, P.S., and Garcia-Blanco, M.A. 2003. Quantification of alternatively spliced FGFR2 RNAs using the RNA invasive cleavage assay. RNA 9: 1552-1561.