A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA)

RNA

Volumn 12, Issue 5, 2006, Pages 913-920

  Castoldi, Mirco ^a,b   Schmidt, Sabine ^b   Benes, Vladimir ^b   Noerholm, Mikkel ^c,d   Kulozik, Andreas E ^a,b   Hentze, Matthias W ^b   Muckenthaler, Martina U ^a,b  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c Exiqon AS   (Denmark)

^d Exiqon A/S   (Denmark)

Author keywords

LNA; Microarrays; microRNAs; Mouse; RNA translation

Indexed keywords

LOCKED NUCLEIC ACID; MICRORNA; NUCLEOTIDE;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENOME ANALYSIS; HYBRIDIZATION; MICROARRAY ANALYSIS; MOLECULAR PROBE; MOLECULAR SIZE; MOUSE; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; SENSITIVITY ANALYSIS;

ANIMALS; BIOPHYSICS; BLOTTING, NORTHERN; DNA PROBES; GENE EXPRESSION PROFILING; MICE; MICE, INBRED C57BL; MICRORNAS; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACIDS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; SENSITIVITY AND SPECIFICITY;

ANIMALIA;

EID: 33646178285     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2332406     Document Type: Article

References (36)

1. Abbott, A.L., Alvarez-Saavedra, E., Miska, E.A., Lau, N.C., Bartel, D.P., Horvitz, H.R., and Ambros, V. 2005. The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev. Cell 9: 403-414.
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. Baskerville, S. and Bartel, D.P. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241-247.
5. Braasch, D.A. and Corey, D.R. 2001. Locked nucleic acid (LNA): Finetuning the recognition of DNA and RNA. Chem. Biol. 8: 1-7.
6. Cai, X., Lu, S., Zhang, Z., Gonzalez, C.M., Damania, B., and Cullen, B.R. 2005. Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proc. Natl. Acad. Sci. 102: 5570-5575.
7. Calin, G.A., Sevignani, C., Dumitru, C.D., Hyslop, T., Noch, E., Yendamuri, S., Shimizu, M., Rattan, S., Bullrich, F., Negrini, M., et al. 2004. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl. Acad. Sci. 101: 2999-3004.
8. Chen, C.Z. and Lodish, H.F. 2005. MicroRNAs as regulators of mammalian hematopoiesis. Semin. Immunol. 17: 155-165.
9. de Moor, C.H., Meijer, H., and Lissenden, S. 2005. Mechanisms of translational control by the 3′ UTR in development and differentiation. Semin. Cell Dev. Biol. 16: 49-58.
10. Doench, J.G. and Sharp, P.A. 2004. Specificity of microRNA target selection in translational repression. Genes & Dev. 18: 504-511.
11. Eckhardt, B.L., Parker, B.S., van Laar, R.K., Restall, C.M., Natoli, A.L., Tavaria, M.D., Stanley, K.L., Sloan, E.K., Moseley, J.M., and Anderson, R.L. 2005. Genomic analysis of a spontaneous model of breast cancer metastasis to bone reveals a role for the extracellular matrix. Mol. Cancer Res. 3: 1-13.
12. Eder, M. and Scherr, M. 2005. MicroRNA and lung cancer. N. Engl. J. Med. 352: 2446-2448.
13. Griffiths-Jones, S. 2004. The microRNA registry. Nucleic Acids Res. 32: D109-D111.
14. Harfe, B.D. 2005. MicroRNAs in vertebrate development. Curr. Opin. Genet. Dev. 15: 410-415.
15. Iorio, M.V., Ferracin, M., Liu, C.G., Veronese, A., Spizzo, R., Sabbioni, S., Magri, E., Pedriali, M., Fabbri, M., Campiglio, M., et al. 2005. MicroRNA gene expression deregulation in human breast cancer. Cancer Res. 65: 7065-7070.
16. Jiang, J., Lee, E.J., Gusev, Y., and Schmittgen, T.D. 2005. Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res. 33: 5394-5403.
17. Jopling, C.L., Yi, M., Lancaster, A.M., Lemon, S.M., and Sarnow, P. 2005. Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science 309: 1577-1581.
18. 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.
19. Leaman, D., Chen, P.Y., Fak, J., Yalcin, A., Pearce, M., Unnerstall, U., Marks, D.S., Sander, C., Tuschl, T., and Gaul, U. 2005. Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell 121: 1097-1108.
20. 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.
21. Lewis, B.P., Burge, C.B., and Bartel, D.P. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
22. Liu, C.G., Calin, G.A., Meloon, B., Gamliel, N., Sevignani, C., Ferracin, M., Dumitru, C.D., Shimizu, M., Zupo, S., Dono, M., et al. 2004. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc. Natl. Acad. Sci. 101: 9740-9744.
23. Lu, J., Getz, G., Miska, E.A., Alvarez-Saavedra, E., Lamb, J., Peck, D., Sweet-Cordero, A., Ebert, B.L., Mak, R.H., Ferrando, A.A., et al. 2005. MicroRNA expression profiles classify human cancers. Nature 435: 834-838.
24. 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.
25. 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.
26. Nelson, P.T., Baldwin, D.A., Kloosterman, W.P., Kauppinen, S., Plasterk, R.H., and Mourelatos, Z. 2006. RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA 12: 187-191.
27. Nielsen, J.T., Stein, P.C., and Petersen, M. 2003. NMR structure of an α-L-LNA:RNA hybrid: Structural implications for RNase H recognition. Nucleic Acids Res. 31: 5858-5867.
28. Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F.A., van Dyk, L.F., Ho, C.K., Shuman, S., Chien, M., et al. 2005. Identification of microRNAs of the herpesvirus family. Nat. Methods 2: 269-276.
29. Schmittgen, T.D., Jiang, J., Liu, Q., and Yang, L. 2004. A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res. 32: e43.
30. 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.
31. Shi, R. and Chiang, V.L. 2005. Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 39: 519-525.
32. Sioud, M. and Rosok, O. 2004. Profiling microRNA expression using sensitive cDNA probes and filter arrays. Biotechniques 37: 574-576, 578-580.
33. Thomsen, R., Nielsen, P.S., and Jensen, T.H. 2005. Dramatically improved RNA in situ hybridization signals using LNA-modified probes. RNA 11: 1145-1148.
34. 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.
35. Tolstrup, N., Nielsen, P.S., Kolberg, J.G., Frankel, A.M., Vissing, H., and Kauppinen, S. 2003. OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Res. 31: 3758-3762.
36. Valoczi, A., Hornyik, C., Varga, N., Burgyan, J., Kauppinen, S., and Havelda, Z. 2004. Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res. 32: e175.