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Evolution of MicroRNAs

  • Protocol
MicroRNA Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 342))

Abstract

MicroRNAs (miRNAs) form a large class of small regulatory RNAs in eukaryotes. Although they share a common processing pathway and certain structural features, in general, there is no detectable sequence similarity among miRNAs from a given organism. On the other hand, many miRNAs are members of a family of a few, often very similar, paralogs. It is, thus, of interest to trace the evolutionary history of individual miRNAs, to identify the timing of gene duplications, and to study relationships between the histories of different miRNA families. Some miRNAs are transcribed from polycistronic primary transcripts. In these cases, we will study the evolution of entire clusters.

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References

  1. Lim, L. P., Lau, N. C., Weinstein, E. G., et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Devel. 17, 991–1008.

    Article  CAS  PubMed  Google Scholar 

  2. Lai, E. C., Tomancak, P., Williams, R. W., and Rubin, G. M. (2003) Computational identificationof Drosophila microRNA genes. Genome Biol. 4, R42.

    Article  PubMed  Google Scholar 

  3. Bonnet, E., Wuyts, J., Rouzé, P., and Van de Peer, Y. (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20, 2911–2917.

    Article  CAS  PubMed  Google Scholar 

  4. Jones-Roades, M. W. and Bartel, D. P. (2004) Computational identification of plant micro-RNAs and their targets, including a stress-induced miRNA. Mol. Cell 14, 787–799.

    Article  Google Scholar 

  5. Adai, A., Johnson, C., Mlotshwa, S., et al. (2005) Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 15, 78–91.

    Article  CAS  PubMed  Google Scholar 

  6. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410.

    CAS  PubMed  Google Scholar 

  7. Legendre, M., Lambert, A., and Gautheret, D. (2005) Profile-based detection of microRNA precursors in animal genomes. Bioinformatics 21, 841–845.

    Article  CAS  PubMed  Google Scholar 

  8. Gautheret, D. and Lambert, A. (2001) Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J. Mol. Biol. 313, 1003–1011.

    Article  CAS  PubMed  Google Scholar 

  9. Thompson, J. D., Higgs, D. G., and Gibson, T. J. (1994) Clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties, and weight matrix choice. Nucl. Acids Res. 22, 4673–4680.

    Article  CAS  PubMed  Google Scholar 

  10. Aiyar, A. (2000) The use of CLUSTAL W and CLUSTAL X for multiple sequence alignment. In: Bioinformatics Methods and Protocols (Misener S. and Krawetz S. A.,eds), Humana, Totowa, NJ, pp. 221–241.

    Google Scholar 

  11. McCaskill, J. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures. Biopolymers 29, 1105–1119.

    Article  CAS  PubMed  Google Scholar 

  12. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415.

    Article  CAS  PubMed  Google Scholar 

  13. Mathews, D., Sabina, J., Zuker, M., and Turner, D. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911–940.

    Article  CAS  PubMed  Google Scholar 

  14. Hofacker, I. L. (2003) Vienna RNA secondary structure server. Nucl. Acids Res. 31, 3429–3431.

    Article  CAS  PubMed  Google Scholar 

  15. Hofacker, I. L., Fekete, M., and Stadler, P. F. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319, 1059–1066.

    Article  CAS  PubMed  Google Scholar 

  16. Felsenstein, J. (1989) PHYLIP-phylogeny inference package (version 3.2). Cladistics 5, 164–166.

    Google Scholar 

  17. Retief, J. D. (2000) Phylogenetic analysis using PHYLIP. In: Bioinformatics Methods and Protocols (Misener S. and Krawetz S. A.,eds), Humana, Totowa, NJ, pp. 243–258.

    Google Scholar 

  18. Tanzer, A. and Stadler, P. F. (2004) Molecular evolution of a microRNA cluster. J. Mol. Biol. 339, 327–335.

    Article  CAS  PubMed  Google Scholar 

  19. Wilbur, W. J. and Lipman, D. J. (1983) Rapid similarity searches of nucleic acid and protein data banks. Proc. Natl. Acad. Sci. USA 80, 726–730.

    Article  CAS  PubMed  Google Scholar 

  20. miRBase, http://microrna.sanger.ac.uk. Last accessed Dec. 27, 2005.

  21. UCSC Genome Bioinformatics. http://genome.ucsc.edu/. Last accessed Dec. 27, 2005.

  22. Noncode. http://www.bioinfo.org.cn/NONCODE/index.htm. Last accessed Dec. 27, 2005.

  23. NCBI. http://www.ncbi.nlm.nih.gov/. Last accessed Dec. 27, 2005.

  24. Ensembl Genome Browser. http://www.ensembl.org/. Last accessed Dec. 27, 2005.

  25. DOE Joint Genome Institute. http://www.jgi.doe.gov/. Last accessed Dec. 27, 2005.

  26. Vienna RNA Package. http://www.tbi.univie.ac.at/RNA/. Last accessed Dec. 27, 2005.

  27. Flamm, C., Hofacker, I. L., and Stadler, P. F. (2004) RNA folding in silico. In: EvolutionaryMethods in Biotechnology (Brakmann S. and Schwienhost A.,eds.), Wiley-VCH, Weinheim, Germany, pp. 177–190.

    Google Scholar 

  28. NCBI ftp site for BLAST executables. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release2.2.6//. Last accessed Dec. 27, 2005.

  29. Bioinformatics at IGBMC, ClustalW ftp site. ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/. Last accessed Dec. 27, 2005.

  30. Bioinformatics at IGBMC, ClustalX ftp site. ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/. Last accessed Dec. 27, 2005.

  31. Bioinformatics at IGBM, ClustalW help. http://bips.u-strasbg.fr/en/Documentation/ClustalW/. Last accessed Dec. 27, 2005.

  32. Bioinformatics at IGBMC, ClustalX help. http://bips.u-strasbg.fr/en/Documentation/ClustalX/. Last accessed Dec. 27, 2005.

  33. PHYLIP. http://evolution.genetics.washington.edu/phylip.html. Last accessed Dec. 27, 2005.

  34. PHYLIP manual. http://evolution.genetics.washington.edu/phylip/doc/main.html. Last accessed Dec. 27, 2005.

  35. NJ Plot at Pole Bioinformatique Lyonnais. http://pbil.univ-lyon1.fr/software/njplot.html. Last accessed Dec. 27, 2005.

  36. Bioinformatics and Evolutionary Genomics, Univ. of Ghent. http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz. Last accessed Dec. 27, 2005.

  37. Cygwin. http://www.cygwin.com/. Last accessed Dec. 27, 2005.

  38. Spanish National Cancer Center (Cluster v.2.5.2). http://bioinfo.cnio.es/~jherrero/downloads/cluster/. Last accessed Dec. 27, 2005.

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Author information

Authors and Affiliations

  1. Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria

    Andrea Tanzer & Peter F. Stadler

Authors
  1. Andrea Tanzer
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  2. Peter F. Stadler
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Editor information

Editors and Affiliations

  1. Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

    Shao-Yao Ying

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© 2006 Humana Press Inc.

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Tanzer, A., Stadler, P.F. (2006). Evolution of MicroRNAs. In: Ying, SY. (eds) MicroRNA Protocols. Methods in Molecular Biology™, vol 342. Humana Press. https://doi.org/10.1385/1-59745-123-1:335

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  • DOI: https://doi.org/10.1385/1-59745-123-1:335

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-581-1

  • Online ISBN: 978-1-59745-123-9

  • eBook Packages: Springer Protocols

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