- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Article Processing Charges ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Recently Accepted Articles ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
Journal of Nucleic Acids
Volume 2010 (2010), Article ID 495904, 10 pages
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.
- V. Ramachandran and X. Chen, “Small RNA metabolism in Arabidopsis,” Trends in Plant Science, vol. 13, no. 7, pp. 368–374, 2008.
- O. Voinnet, “Origin, biogenesis, and activity of plant microRNAs,” Cell, vol. 136, no. 4, pp. 669–687, 2009.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- I. L. Hofacker, “Vienna RNA secondary structure server,” Nucleic Acids Research, vol. 31, no. 13, pp. 3429–3431, 2003.
- 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.
- S. R. Eddy, “SQUID—C function library for sequence analysis,” 2008, http://selab.janelia.org/software.html#squid.
- A. F. A. Smit, R. Hubley, and P. Green, “RepeatMasker Open-3.0,” 2004, http://www.repeatmasker.org/.
- 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.
- 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.
- R. Giegerich, B. Voß, and M. Rehmsmeier, “Abstract shapes of RNA,” Nucleic Acids Research, vol. 32, no. 16, pp. 4843–4851, 2004.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- E. M. Tsagris, Á. E. M. de Alba, M. Gozmanova, and K. Kalantidis, “Viroids,” Cellular Microbiology, vol. 10, no. 11, pp. 2168–2179, 2008.
- 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.
- M. Schmitz and G. Steger, “Potato spindle tuber viroid (PSTVd),” Plant Viruses, vol. 1, pp. 106–115, 2007.
- 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.
- 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.
- 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.
- 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.