miRBase: microRNA Sequences and Annotation

Sam Griffiths‐Jones1

1 University of Manchester, Manchester, United Kingdom
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 12.9
DOI:  10.1002/0471250953.bi1209s29
Online Posting Date:  March, 2010
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Abstract

miRBase is the central repository for microRNA (miRNA) sequence information. miRBase has a role in defining the nomenclature for miRNA genes and assigning names to novel miRNAs for publication in peer‐reviewed journals. The online miRBase database is a resource containing all published miRNA sequences, together with textual annotation and links to the primary literature and to other secondary databases. The database provides a variety of methods to query the data, by specific searches of sequences and associated text and literature. All miRBase data are also available for download from the miRBase FTP site. Curr. Protoc. Bioinform. 29:12.9.1‐12.9.10. © 2010 by John Wiley & Sons, Inc.

Keywords: microRNA; miRNA; miRBase

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Retrieving microRNA Sequences and Annotation via the miRBase Web Interface
  • Alternate Protocol 1: Local Searches of Downloaded miRNA Sequences
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

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Literature Cited

Literature Cited
   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.
   Ambros, V., Bartel, B., Bartel, D.P., Burge, C.B., Carrington, J.C., Chen, X., Dreyfuss, G., Eddy, S.R., Griffiths‐Jones, S., Marshall, M., Matzke, M., Ruvkun, G., and Tuschl, T. 2003. A uniform system for microRNA annotation. RNA 9:277‐279.
   Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116:281‐297.
   Bartel, D.P. 2009. MicroRNAs: Target recognition and regulatory functions. Cell 136:215‐233.
   Caudy, A.A., Myers, M., Hannon, G.J., and Hammond, S.M. 2002. Fragile X‐related protein and VIG associate with the RNA interference machinery. Genes Dev. 16:2491‐2496.
   Friedman, R.C., Farh, K.K., Burge, C.B., and Bartel, D.P. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19:92‐105.
   Griffiths‐Jones, S. 2004. The microRNA Registry. Nucleic Acids Res. 32:D109‐D111.
   Griffiths‐Jones, S., Grocock, R.J., van Dongen, S., Bateman, A., and Enright, A.J. 2006. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34:D140‐D144.
   Griffiths‐Jones, S., Saini, H.K., van Dongen, S., and Enright, A.J. 2008. miRBase: Tools for microRNA genomics. Nucleic Acids Res. 36:D154‐D158.
   Kent, W.J. 2002. BLAT: The BLAST‐like alignment tool. Genome Res. 12:656‐664.
   Lagos‐Quintana, M., Rauhut, R., Lendeckel, W., Tuschl, T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294:853‐858.
   Lau, N.C., Lim, L.P., Weinstein, E.G., and Bartel, D.P. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858‐862.
   Lee, R.C. and Ambros, V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862‐864.
   Lee, Y., Jeon, K., Lee, J., Kim, S., and Kim, V.N. 2002. MicroRNA maturation: Stepwise processing and subcellular localization. EMBO J. 21:4663‐4670.
   Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Rådmark, O., Kim, S., and Kim, V.N. 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415‐419.
   Lee, Y., Kim, M., Han, J., Yeom, K., Lee, S., Baek, S.H., and Kim, V.N. 2004. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23:4051‐4060.
   Lewis, B.P., Burge, C.B., and Bartel, D.P. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15‐20.
   Llave, C., Xie, Z., Kasschau, K.D., and Carrington, J.C. 2002. Cleavage of Scarecrow‐like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053‐2056.
   Meyers, B.C., Axtell, M.J., Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., Griffiths‐Jones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qi, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Weigel, D., and Zhu, J. 2008. Criteria for annotation of plant MicroRNAs. Plant Cell 20:3186‐3190.
   Negrini, M., Nicoloso, M.S., and Calin, G.A. 2009. MicroRNAs and cancer–new paradigms in molecular oncology. Curr. Opin. Cell Biol. 21:470‐479.
   Pearson, W. 2004. Finding protein and nucleotide similarities with FASTA. Curr. Protoc. Bioinform. 8:3.9.1‐3.9.23.
   Prüfer, K., Stenzel, U., Dannemann, M., Green, R.E., Lachmann, M., and Kelso, J. 2008. PatMaN: Rapid alignment of short sequences to large databases. Bioinformatics 24:1530‐1531.
   Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P. 2002. MicroRNAs in plants. Genes Dev. 16:1616‐1626.
   Rodriguez, A., Griffiths‐Jones, S., Ashurst, J.L., and Bradley, A. 2004. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14:1902‐1910.
   Saini, H.K., Griffiths‐Jones, S., and Enright, A.J. 2007. Genomic analysis of human microRNA transcripts. Proc. Natl. Acad. Sci. U.S.A. 104:17719‐17724.
   Saini, H.K., Enright, A.J., and Griffiths‐Jones, S. 2008. Annotation of mammalian primary microRNAs. BMC Genomics 9:564.
   Saunders, M.A. and Lim, LP. 2009. (micro)Genomic medicine: microRNAs as therapeutics and biomarkers. RNA Biol. 6:324‐328.
   Sethupathy, P., Corda, B., and Hatzigeorgiou, A.G. 2006a. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 12:192‐197.
   Sethupathy, P., Megraw, M., and Hatzigeorgiou, A.G. 2006b. A guide through present computational approaches for the identification of mammalian microRNA targets. Nat. Methods 3:881‐886.
   Stefani, G. and Slack, F.J. 2008. Small non‐coding RNAs in animal development. Nat. Rev. Mol. Cell Biol. 9:219‐230.
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