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Journal of Nucleic Acids
Volume 2012 (2012), Article ID 283560, 10 pages
http://dx.doi.org/10.1155/2012/283560
Research Article

Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray

1Section for Genomics and RNomics, Biocenter, Innsbruck Medical University, Fritz Pregl Strasse 3, 6020 Innsbruck, Austria
2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
3Université de Lorraine, CNRS-UMR 7214 AREMS, 9 avenue de la Forêt de Haye, F-54506 Vandoeuvre-lès-Nancy, France

Received 30 November 2011; Revised 6 March 2012; Accepted 6 March 2012

Academic Editor: Ashis K. Basu

Copyright © 2012 Konstantinia Skreka et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. E. Birney, J. A. Stamatoyannopoulos, A. Dutta et al., “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project,” Nature, vol. 447, no. 7146, pp. 799–816, 2007. View at Publisher · View at Google Scholar · View at Scopus
  2. J. S. Mattick and I. V. Makunin, “Small regulatory RNAs in mammals,” Human Molecular Genetics, vol. 14, no. 1, pp. R121–R132, 2005. View at Publisher · View at Google Scholar · View at Scopus
  3. J. S. Mattick and I. V. Makunin, “Non-coding RNA,” Human Molecular Genetics, vol. 15, pp. R17–R29, 2006. View at Publisher · View at Google Scholar · View at Scopus
  4. A. T. Willingham and T. R. Gingeras, “TUF Love for “Junk” DNA,” Cell, vol. 125, no. 7, pp. 1215–1220, 2006. View at Publisher · View at Google Scholar · View at Scopus
  5. A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, “Mapping and quantifying mammalian transcriptomes by RNA-Seq,” Nature Methods, vol. 5, no. 7, pp. 621–628, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. A. Saxena and P. Carninci, “Whole transcriptome analysis: what are we still missing?” Wiley Interdisciplinary Reviews, vol. 3, no. 5, pp. 527–543, 2011. View at Publisher · View at Google Scholar · View at Scopus
  7. C. A. Raabe, C. H. Hoe, G. Randau, J. Brosius, T. H. Tang, and T. S. Rozhdestvensky, “The rocks and shallows of deep RNA sequencing: examples in the Vibrio cholerae RNome,” RNA, vol. 17, no. 7, pp. 1357–1366, 2011. View at Publisher · View at Google Scholar · View at Scopus
  8. M. Castoldi, S. Schmidt, V. Benes, M. W. Hentze, and M. U. Muckenthaler, “miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes,” Nature Protocols, vol. 3, no. 2, pp. 321–329, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. M. Hackl, S. Brunner, K. Fortschegger et al., “miR-17, miR-19b, miR-20a, and miR-106a are down-regulated in human aging,” Aging Cell, vol. 9, no. 2, pp. 291–296, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. N. Jacobsen, J. Bentzen, M. Meldgaard et al., “LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E.,” Nucleic Acids Research, vol. 30, no. 19, article e100, 2002. View at Scopus
  11. R. N. Veedu and J. Wengel, “Locked nucleic acids: promising nucleic acid analogs for therapeutic applications,” Chemistry and Biodiversity, vol. 7, no. 3, pp. 536–542, 2010. View at Publisher · View at Google Scholar · View at Scopus
  12. J. Liao, L. Yu, Y. Mei et al., “Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer,” Molecular Cancer, vol. 9, article 198, 2010. View at Publisher · View at Google Scholar · View at Scopus
  13. X. Liu, K. Fortin, and Z. Mourelatos, “MicroRNAs: biogenesis and molecular functions,” Brain Pathology, vol. 18, no. 1, pp. 113–121, 2008. View at Publisher · View at Google Scholar · View at Scopus
  14. N. Rosenfeld, R. Aharonov, E. Meiri et al., “MicroRNAs accurately identify cancer tissue origin,” Nature Biotechnology, vol. 26, no. 4, pp. 462–469, 2008. View at Publisher · View at Google Scholar · View at Scopus
  15. K. Skreka, M. Karbiener, M. Zywicki, H. Alexander, S. Marcel, and R. Mathieu, “Expression profiling of ncRNAs employing RNP libraries and custom LNA/DNA microarray analysis,” Regulatory RNAs: Basics, Methods and Applications, Springer, 2012.
  16. M. Rederstorff, S. H. Bernhart, A. Tanzer et al., “RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles.,” Nucleic Acids Research, vol. 38, no. 10, article e113, 2010. View at Publisher · View at Google Scholar · View at Scopus
  17. M. W. Pfaffl, “A new mathematical model for relative quantification in real-time RT-PCR,” Nucleic Acids Research, vol. 29, no. 9, article e45, 2001. View at Scopus
  18. R. Hutzinger, J. Mrázek, S. Vorwerk, and A. Hüttenhofer, “NcRNA-microchip analysis: a novel approach to identify differential expression of non-coding RNAs,” RNA Biology, vol. 7, no. 5, pp. 586–595, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. H. Fang, X. Fan, L. Guo et al., “Self-self hybridization as an alternative experiment design to dye swap for two-color microarrays,” OMICS A Journal of Integrative Biology, vol. 11, no. 1, pp. 14–24, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. J. Lingner, I. Radtke, E. Wahle, and W. Keller, “Purification and characterization of poly(A) polymerase from Saccharomyces cerevisiae,” The Journal of Biological Chemistry, vol. 266, no. 14, pp. 8741–8746, 1991. View at Scopus
  21. W. A. Cantara, P. F. Crain, J. Rozenski et al., “The RNA modification database, RNAMDB: 2011 update,” Nucleic Acids Research, vol. 39, no. 1, pp. D195–D201, 2011. View at Publisher · View at Google Scholar · View at Scopus
  22. I. Behm-Ansmant, M. Helm, and Y. Motorin, “Use of specific chemical reagents for detection of modified nucleotides in RNA,” Journal of Nucleic Acids, vol. 2011, Article ID 408053, 17 pages, 2011. View at Publisher · View at Google Scholar
  23. R. Ishitani, S. Yokoyama, and O. Nureki, “Structure, dynamics, and function of RNA modification enzymes,” Current Opinion in Structural Biology, vol. 18, no. 3, pp. 330–339, 2008. View at Publisher · View at Google Scholar · View at Scopus
  24. Y. Wang and R. Blelloch, “Cell cycle regulation by microRNAs in stem cells,” Results Probl Cell Differ, vol. 53, pp. 459–472, 2010.
  25. A. Rybak, H. Fuchs, L. Smirnova et al., “A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment,” Nature Cell Biology, vol. 10, no. 8, pp. 987–993, 2008. View at Publisher · View at Google Scholar · View at Scopus
  26. F. G. Wulczyn, L. Smirnova, A. Rybak et al., “Post-transcriptional regulation of the let-7 microRNA during neural cell specification,” The FASEB Journal, vol. 21, no. 2, pp. 415–426, 2007. View at Publisher · View at Google Scholar · View at Scopus
  27. C. Ender, A. Krek, M. R. Friedländer et al., “A Human snoRNA with MicroRNA-Like Functions,” Molecular Cell, vol. 32, no. 4, pp. 519–528, 2008. View at Publisher · View at Google Scholar · View at Scopus
  28. S. Kishore, A. Khanna, Z. Zhang et al., “The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing,” Human Molecular Genetics, vol. 19, no. 7, Article ID ddp585, pp. 1153–1164, 2010. View at Publisher · View at Google Scholar · View at Scopus
  29. S. Kishore and S. Stamm, “The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C,” Science, vol. 311, no. 5758, pp. 230–232, 2006. View at Publisher · View at Google Scholar · View at Scopus
  30. A. A. Saraiya and C. C. Wang, “snoRNA, a novel precursor of microRNA in Giardia lamblia,” PLoS Pathogens, vol. 4, no. 11, Article ID e1000224, 2008. View at Publisher · View at Google Scholar · View at Scopus
  31. R. J. Taft, E. A. Glazov, T. Lassmann, Y. Hayashizaki, P. Carninci, and J. S. Mattick, “Small RNAs derived from snoRNAs,” RNA, vol. 15, no. 7, pp. 1233–1240, 2009. View at Publisher · View at Google Scholar · View at Scopus
  32. S. Gilad, E. Meiri, Y. Yogev et al., “Serum microRNAs are promising novel biomarkers,” PLoS One, vol. 3, no. 9, Article ID e3148, 2008. View at Publisher · View at Google Scholar · View at Scopus
  33. J. Lu, G. Getz, E. A. Miska et al., “MicroRNA expression profiles classify human cancers,” Nature, vol. 435, no. 7043, pp. 834–838, 2005. View at Publisher · View at Google Scholar · View at Scopus
  34. R. A. Gupta, N. Shah, K. C. Wang et al., “Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis,” Nature, vol. 464, no. 7291, pp. 1071–1076, 2010. View at Publisher · View at Google Scholar · View at Scopus
  35. M. Huarte and J. L. Rinn, “Large non-coding RNAs: missing links in cancer?” Human Molecular Genetics, vol. 19, no. 2, pp. R152–R161, 2010. View at Scopus
  36. J. Kocerha, S. Kauppinen, and C. Wahlestedt, “microRNAs in CNS disorders,” Neuromolecular Medicine, vol. 11, no. 3, pp. 162–172, 2009. View at Scopus
  37. M. Rederstorff and A. Hüttenhofer, “Small non-coding RNAs in disease development and host-pathogen interactions,” Current Opinion in Molecular Therapeutics, vol. 12, no. 6, pp. 684–694, 2010. View at Scopus