About this Journal Submit a Manuscript Table of Contents
Journal of Nucleic Acids
Volume 2010 (2010), Article ID 495904, 10 pages
http://dx.doi.org/10.4061/2010/495904
Research Article

NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome

Institut für Physikalische Biologie, Universitätsstr. 1, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany

Received 25 March 2010; Revised 10 June 2010; Accepted 29 June 2010

Academic Editor: Ben Berkhout

Copyright © 2010 Jan-Hendrik Teune and Gerhard Steger. 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. V. Ramachandran and X. Chen, “Small RNA metabolism in Arabidopsis,” Trends in Plant Science, vol. 13, no. 7, pp. 368–374, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  2. O. Voinnet, “Origin, biogenesis, and activity of plant microRNAs,” Cell, vol. 136, no. 4, pp. 669–687, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  3. V. Ambros, “A hierarchy of regulatory genes controls a larva-to-adult developmental switch in C. elegans,” Cell, vol. 57, no. 1, pp. 49–57, 1989. View at Scopus
  4. B. J. Reinhart, F. J. Slack, M. Basson et al., “The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans,” Nature, vol. 403, no. 6772, pp. 901–906, 2000. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  5. J. R. Brown and P. Sanseau, “A computational view of microRNAs and their targets,” Drug Discovery Today, vol. 10, no. 8, pp. 595–601, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  6. N. D. Mendes, A. T. Freitas, and M.-F. Sagot, “Current tools for the identification of miRNA genes and their targets,” Nucleic Acids Research, vol. 37, no. 8, pp. 2419–2433, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  7. M. Yousef, L. Showe, and M. Showe, “A study of microRNAs in silico and in vivo: bioinformatics approaches to microRNA discovery and target identification,” FEBS Journal, vol. 276, no. 8, pp. 2150–2156, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  8. W. Ritchie, M. Legendre, and D. Gautheret, “RNA stem-loops: to be or not to be cleaved by RNAse III,” RNA, vol. 13, no. 4, pp. 457–462, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  9. T. Dezulian, M. Remmert, J. F. Palatnik, D. Weigel, and D. H. Huson, “Identification of plant microRNA homologs,” Bioinformatics, vol. 22, no. 3, pp. 359–360, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  10. S. Pfeffer, A. Sewer, M. Lagos-Quintana et al., “Identification of microRNAs of the herpesvirus family,” Nature Methods, vol. 2, no. 4, pp. 269–276, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  11. X. J. Wang, J. L. Reyes, N. H. Chua, and T. Gaasterland, “Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets,” Genome Biology, vol. 5, no. 9, p. R65, 2004. View at Scopus
  12. M. W. Jones-Rhoades and D. P. Bartel, “Computational identification of plant microRNAs and their targets, including a stress-induced miRNA,” Molecular Cell, vol. 14, no. 6, pp. 787–799, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  13. S. Kadri, V. Hinman, and P. V. Benos, “HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models,” BMC Bioinformatics, vol. 10, no. 1, article S35, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  14. C. Xue, F. Li, T. He, G.-P. Liu, Y. Li, and X. Zhang, “Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine,” BMC Bioinformatics, vol. 6, article 310, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  15. S. Griffiths-Jones, R. J. Grocock, S. van Dongen, A. Bateman, and A. J. Enright, “miRBase: microRNA sequences, targets and gene nomenclature,” Nucleic Acids Research, vol. 34, pp. D140–D144, 2006. View at Scopus
  16. S. Griffiths-Jones, H. K. Saini, S. Van Dongen, and A. J. Enright, “miRBase: tools for microRNA genomics,” Nucleic Acids Research, vol. 36, no. 1, pp. D154–D158, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  17. B. H. Zhang, X. P. Pan, S. B. Cox, G. P. Cobb, and T. A. Anderson, “Evidence that miRNAs are different from other RNAs,” Cellular and Molecular Life Sciences, vol. 63, no. 2, pp. 246–254, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  18. I. L. Hofacker, “Vienna RNA secondary structure server,” Nucleic Acids Research, vol. 31, no. 13, pp. 3429–3431, 2003. View at Publisher · View at Google Scholar · View at Scopus
  19. S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S. R. Eddy, and A. Bateman, “Rfam: annotating non-coding RNAs in complete genomes,” Nucleic Acids Research, vol. 33, pp. D121–D124, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  20. S. R. Eddy, “SQUID—C function library for sequence analysis,” 2008, http://selab.janelia.org/software.html#squid.
  21. A. F. A. Smit, R. Hubley, and P. Green, “RepeatMasker Open-3.0,” 2004, http://www.repeatmasker.org/.
  22. K. L. S. Ng and S. K. Mishra, “De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures,” Bioinformatics, vol. 23, no. 11, pp. 1321–1330, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  23. M. Garcia-Hernandez, T. Z. Berardini, G. Chen et al., “TAIR: a resource for integrated Arabidopsis data,” Functional and Integrative Genomics, vol. 2, no. 6, pp. 239–253, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  24. R. Giegerich, B. Voß, and M. Rehmsmeier, “Abstract shapes of RNA,” Nucleic Acids Research, vol. 32, no. 16, pp. 4843–4851, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  25. P. Steffen, B. Voß, M. Rehmsmeier, J. Reeder, and R. Giegerich, “RNAshapes: an integrated RNA analysis package based on abstract shapes,” Bioinformatics, vol. 22, no. 4, pp. 500–503, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  26. I. L. Hofacker, B. Priwitzer, and P. F. Stadler, “Prediction of locally stable RNA secondary structures for genome-wide surveys,” Bioinformatics, vol. 20, no. 2, pp. 186–190, 2004. View at Publisher · View at Google Scholar · View at Scopus
  27. J.-W. Nam, K.-R. Shin, J. Han, Y. Lee, V. N. Kim, and B.-T. Zhang, “Human microRNA prediction through a probabilistic co-learning model of sequence and structure,” Nucleic Acids Research, vol. 33, no. 11, pp. 3570–3581, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  28. A. M. Gustafson, E. Allen, S. Givan, D. Smith, J. C. Carrington, and K. D. Kasschau, “ASRP: the Arabidopsis Small RNA Project database,” Nucleic Acids Research, vol. 33, pp. D637–D640, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  29. T. W. H. Backman, C. M. Sullivan, J. S. Cumbie et al., “Update of ASRP: the Arabidopsis Small RNA Project database,” Nucleic Acids Research, vol. 36, no. 1, pp. D982–D985, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  30. B. D. Pant, M. Musialak-Lange, P. Nuc et al., “Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing,” Plant Physiology, vol. 150, no. 3, pp. 1541–1555, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  31. N. Fahlgren, C. M. Sullivan, K. D. Kasschau et al., “Computational and analytical framework for small RNA profiling by high-throughput sequencing,” RNA, vol. 15, no. 5, pp. 992–1002, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  32. G. Steger and D. Riesner, “Properties of viroids: molecular characteristics,” in Viroids, A. Hadidi, R. Flores, J. W. Randles, and J. S. Semancik, Eds., pp. 15–29, CSIRO Publishing, Melbourne, Australia, 2003.
  33. H. J. Gross, H. Domdey, C. Lossow, et al., “Nucleotide sequence and secondary structure of potato spindle tuber viroid,” Nature, vol. 273, no. 5659, pp. 203–208, 1978.
  34. P. Keese and R. H. Symons, “Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 82, no. 14, pp. 4582–4586, 1985.
  35. N. Kolonko, O. Bannach, K. Aschermann et al., “Transcription of potato spindle tuber viroid by RNA polymerase II starts in the left terminal loop,” Virology, vol. 347, no. 2, pp. 392–404, 2006. View at Publisher · View at Google Scholar · View at PubMed
  36. B. Li, W. Yin, and X. Xia, “Identification of microRNAs and their targets from Populus euphratica,” Biochemical and Biophysical Research Communications, vol. 388, no. 2, pp. 272–277, 2009. View at Publisher · View at Google Scholar · View at PubMed
  37. L. I. Shukla, V. Chinnusamy, and R. Sunkar, “The role of microRNAs and other endogenous small RNAs in plant stress responses,” Biochimica et Biophysica Acta, vol. 1779, no. 11, pp. 743–748, 2008. View at Publisher · View at Google Scholar · View at PubMed
  38. G. Jagadeeswaran, A. Saini, and R. Sunkar, “Biotic and abiotic stress down-regulate miR398 expression in Arabidopsis,” Planta, vol. 229, no. 4, pp. 1009–1014, 2009. View at Publisher · View at Google Scholar · View at PubMed
  39. M. J. Axtell and J. L. Bowman, “Evolution of plant microRNAs and their targets,” Trends in Plant Science, vol. 13, no. 7, pp. 343–349, 2008. View at Publisher · View at Google Scholar · View at PubMed
  40. E. M. Tsagris, Á. E. M. de Alba, M. Gozmanova, and K. Kalantidis, “Viroids,” Cellular Microbiology, vol. 10, no. 11, pp. 2168–2179, 2008. View at Publisher · View at Google Scholar · View at PubMed
  41. B. Ding and A. Itaya, “Viroid: a useful model for studying the basic principles of infection and RNA biology,” Molecular Plant-Microbe Interactions, vol. 20, no. 1, pp. 7–20, 2007. View at Publisher · View at Google Scholar · View at PubMed
  42. M. Schmitz and G. Steger, “Potato spindle tuber viroid (PSTVd),” Plant Viruses, vol. 1, pp. 106–115, 2007.
  43. J.-A. Daròs, S. F. Elena, and R. Flores, “Viroids: an Ariadne's thread into the RNA labyrinth,” EMBO Reports, vol. 7, no. 6, pp. 593–598, 2006. View at Publisher · View at Google Scholar · View at PubMed
  44. T. Baumstark, A. R. W. Schröder, and D. Riesner, “Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation,” EMBO Journal, vol. 16, no. 3, pp. 599–610, 1997. View at Publisher · View at Google Scholar · View at PubMed
  45. A. Itaya, X. Zhong, R. Bundschuh et al., “A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation,” Journal of Virology, vol. 81, no. 6, pp. 2980–2994, 2007. View at Publisher · View at Google Scholar · View at PubMed
  46. F. Di Serio, A.-E. M. De Alba, B. Navarro, A. Gisel, and R. Flores, “RNA-dependent RNA polymerase 6 delays accumulation and precludes meristem invasion of a viroid that replicates in the nucleus,” Journal of Virology, vol. 84, no. 5, pp. 2477–2489, 2010. View at Publisher · View at Google Scholar · View at PubMed