MicroRNA or Not MicroRNA?

  • David Langenberger
  • Sebastian Bartschat
  • Jana Hertel
  • Steve Hoffmann
  • Hakim Tafer
  • Peter F. Stadler
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6832)

Abstract

The avalanche of next generation sequencing data has led to a rapid increase of annotated microRNAs in the last few years. Many of them are specific to individual species or rather narrow clades. A closer inspection of the current version of miRBase shows that dozens of entries conflict with other ncRNAs, in particular snoRNAs. With few exceptions, these cases show little similarities to canonical microRNAs, however, and thus they should be considered as mis-annotations.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Terns, M.P., Terns, R.M.: Small nucleolar RNAs: versatile trans-acting molecules of ancient evolutionary origin. Gene Expr. 10, 17–39 (2002)Google Scholar
  2. 2.
    Kawaji, H., Nakamura, M., Takahashi, Y., Sandelin, A., Katayama, S., Email, F.S., Daub, C., Kai, C., Jun Kawai, J., Yasuda, J., Carninci, P., Hayashizaki, Y.: Hidden layers of human small RNAs. BMC Genomics 9, 157 (2008)CrossRefGoogle Scholar
  3. 3.
    Taft, R.J., Glazov, E.A., Lassmann, T., Hayashizaki, Y., Carninci, P., Mattick, J.S.: Small RNAs derived from snoRNAs. RNA 15, 1233–1240 (2009)CrossRefGoogle Scholar
  4. 4.
    Langenberger, D., Bermudez-Santana, C., Stadler, P.F., Hoffmann, S.: Identification and classification of small RNAs in transcriptome sequence data. In: Pac. Symp. Biocomput., vol. 15, pp. 80–87 (2010)Google Scholar
  5. 5.
    Brameier, M., Herwig, A., Reinhardt, R., Walter, L., Gruber, J.: Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res. 39, 675–686 (2011)CrossRefGoogle Scholar
  6. 6.
    Ender, C., Krek, A., Friedländer, M.R., Beitzinger, M., Weinmann, L., Chen, W., Pfeffer, S., Rajewsky, N., Meister, G.: A human snoRNA with microRNA-like functions. Mol. Cell 32, 519–528 (2008)CrossRefGoogle Scholar
  7. 7.
    Meiri, E., Levy, A., Benjamin, H., Ben-David, M., Cohen, L., Dov, A., Dromi, N., Elyakim, E., Yerushalmi, N., Zion, O., Lithwick-Yanai, G., Sitbon, E.: Discovery of microRNAs and other small RNAs in solid tumors. Nucleic Acids Res. 38, 6234–6246 (2010)CrossRefGoogle Scholar
  8. 8.
    Stadler, P.F., Chen, J.J.L., Hackermüller, J., Hoffmann, S., Horn, F., Khaitovich, P., Kretzschmar, A.K., Mosig, A., Prohaska, S.J., Qi, X., Schutt, K., Ullmann, K.: Evolution of vault RNAs. Mol. Biol. Evol. 26, 1975–1991 (2009)CrossRefGoogle Scholar
  9. 9.
    Persson, H., Kvist, A., Vallon-Christersson, J., Medstrand, P., Borg, A., Rovira, C.: The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs. Nat. Cell Biol. 11, 1268–1271 (2009)CrossRefGoogle Scholar
  10. 10.
    Mosig, A., Stadler, P.F.: Evolution of vault RNAs. In: N, N. (ed.) Encyclopedia of Life Sciences, Wiley-Blackwell, Hoboken, NJ (2011), doi:10.1002/9780470015902.a0022883Google Scholar
  11. 11.
    Lee, Y.S., Shibata, Y., Malhotra, A., Dutta, A.: A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev. 23, 2639–2649 (2009)CrossRefGoogle Scholar
  12. 12.
    Cole, C., Sobala, A., Lu, C., Thatcher, S.R., Bowman, A., Brown, J.W., Green, P.J., Barton, G.J., Hutvagner, G.: Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 15, 2147–2160 (2009)CrossRefGoogle Scholar
  13. 13.
    Haussecker, D., Huang, Y., Lau, A., Parameswaran, P., Fire, A.Z., Kay, M.A.: Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16, 673–695Google Scholar
  14. 14.
    Findeiß, S., Langenberger, D., Stadler, P.F., Hoffmann, S.: Traces of post-transcriptional RNA modifications in deep sequencing data. Biol. Chem. 392, 305–313 (2011)CrossRefGoogle Scholar
  15. 15.
    Schopman, N.C.T., Heynen, S., Haasnoot, J., Berkhout, B.: A miRNA-tRNA mix-up: tRNA origin of proposed miRNA. RNA Biology 7, 573–576 (2010)CrossRefGoogle Scholar
  16. 16.
    Miyoshi, K., Miyoshi, T., Siomi, H.: Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production. Mol. Genet. Genomics 284, 95–103 (2010)CrossRefGoogle Scholar
  17. 17.
    Borchert, G.M., Lanier, W., Davidson, B.L.: RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol. 13, 1097–1101 (2006)CrossRefGoogle Scholar
  18. 18.
    Bortolin-Cavaillé, M.L., Dance, M., Weber, M., Cavaillé, J.: C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts. Nucleic Acids Res. 37, 3464–3473 (2009)CrossRefGoogle Scholar
  19. 19.
    Canella, D., Praz, V., Reina, J.H., Cousin, P., Hernandez, N.: Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res. 20, 710–721 (2010)CrossRefGoogle Scholar
  20. 20.
    Berezikov, E., Chung, W.J., Willis, J., Cuppen, E., Lai, E.C.: Mammalian mirtron genes. Mol. Cell 28, 328–336 (2007)CrossRefGoogle Scholar
  21. 21.
    Okamura, K., Hagen, J.W., Duan, H., Tyler, D.M., Lai, E.C.: The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130, 89–100 (2007)CrossRefGoogle Scholar
  22. 22.
    Ruby, G.J., Jan, C.H., Bartell, D.P.: Intronic microRNA precursors that bypass Drosha processing. Nature 48, 83–86 (2007)CrossRefGoogle Scholar
  23. 23.
    Chung, W.J., Agius, P., Westholm, J.O., Chen, M., Okamura, K., Robine, N., Leslie, C.S., Lai, E.C.: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. Genome Res. 21, 286–300 (2011)CrossRefGoogle Scholar
  24. 24.
    Flynt, A.S., Greimann, J.C., Chung, W.J., Lima, C.D., Lai, E.C.: MicroRNA biogenesis via splicing and exosome-mediated trimming in Drosophila. Mol. Cell 38, 900–907 (2010)CrossRefGoogle Scholar
  25. 25.
    Chong, M.M.W., Zhang, G., Cheloufi, S., Neubert, T.A., Hannon, G.J., Littman, D.R.: Canonical and alternate functions of the microRNA biogenesis machinery. Genes Dev. 24, 1951–1960 (2010)CrossRefGoogle Scholar
  26. 26.
    Scott, M.S., Avolio, F., Ono, M., Lamond, A.I., Barton, G.J.: Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput. Biol. 5, e100050 (2009)CrossRefGoogle Scholar
  27. 27.
    Politz, J.C., Hogan, E.M., Pederson, T.: MicroRNAs with a nucleolar location. RNA 15, 1705–1715 (2009)CrossRefGoogle Scholar
  28. 28.
    Griffiths-Jones, S.: The microRNA Registry. Nucleic Acids Res. 32, D109–D111 (2004)CrossRefGoogle Scholar
  29. 29.
    Mosig, A., Guofeng, M., Stadler, B.M.R., Stadler, P.F.: Evolution of the vertebrate Y RNA cluster. Th. Biosci. 126, 9–14 (2007)CrossRefGoogle Scholar
  30. 30.
    Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A., Eddy, S.R.: Rfam: an RNA family database. Nucleic Acids Res. 31, 439–441 (2003)CrossRefGoogle Scholar
  31. 31.
    Hoffmann, S., Otto, C., Kurtz, S., Sharma, C., Khaitovich, P., Vogel, J., Stadler, P.F., Hackermüller, J.: Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comp. Biol. 5, e1000502 (2009)CrossRefGoogle Scholar
  32. 32.
    Weber, M.J.: Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genet. 2, e205 (2006)CrossRefGoogle Scholar
  33. 33.
    Schmitz, J., Zemann, A., Churakov, G., Kuhl, H., Grützner, F., Reinhardt, R., Brosius, J.: Retroposed SNOfall–a mammalian-wide comparison of platypus snoRNAs. Genome Res. 18, 1005–1010 (2008)CrossRefGoogle Scholar
  34. 34.
    Smalheiser, N.R., Torvik, V.I.: Mammalian microRNAs derived from genomic repeats. Trends Genet. 21, 322–326 (2005)CrossRefGoogle Scholar
  35. 35.
    Hertel, J., Stadler, P.F.: Hairpins in a haystack: Recognizing microRNA precursors in comparative genomics data. Bioinformatics 22, e197–e202 (2006)CrossRefGoogle Scholar
  36. 36.
    Hertel, J., Hofacker, I.L., Stadler, P.F.: snoReport: Computational identification of snoRNAs with unknown targets. Bioinformatics 24, 158–164 (2008)CrossRefGoogle Scholar
  37. 37.
    Hertel, J., Lindemeyer, M., Missal, K., Fried, C., Tanzer, A., Flamm, C., Hofacker, I.L., Stadler, P.F.: Students of Bioinformatics Computer Labs 2004 & 2005: The expansion of the metazoan microRNA repertoire. BMC Genomics 7, 15 (2006)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • David Langenberger
    • 1
    • 2
    • 3
  • Sebastian Bartschat
    • 1
  • Jana Hertel
    • 1
    • 2
  • Steve Hoffmann
    • 3
    • 2
  • Hakim Tafer
    • 1
    • 2
  • Peter F. Stadler
    • 1
    • 2
    • 3
    • 4
    • 5
    • 6
    • 7
    • 8
  1. 1.Bioinformatics Group, Department of Computer ScienceUK
  2. 2.Interdisciplinary Center for BioinformaticsUniversity of LeipzigLeipzigGermany
  3. 3.LIFE – Leipzig Research Center for Civilization DiseasesUniversity of LeipzigGermany
  4. 4.Max Planck Institute for Mathematics in the SciencesLeipzigGermany
  5. 5.Fraunhofer Institut für Zelltherapie und ImmunologieLeipzigGermany
  6. 6.Department of Theoretical ChemistryUniversity of ViennaWienAustria
  7. 7.Center for non-coding RNA in Technology and HealthUniversity of CopenhagenFrederiksberg CDenmark
  8. 8.Santa Fe InstituteSanta FeUSA

Personalised recommendations