Identification of Novel and Known miRNAs in Deep‐Sequencing Data with miRDeep2

Sebastian D. Mackowiak1

1 Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 12.10
DOI:  10.1002/0471250953.bi1210s36
Online Posting Date:  December, 2011
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miRNAs comprise an abundant class of small non‐coding RNAs that play important roles in a wide range of biological processes by post‐transcriptional regulation of a large fraction of animal genes. High‐throughput sequencing machines and the availability of completely sequenced genomes make it possible to reliably identify miRNAs with computational methods. This unit documents how to use the miRDeep2 software package to identify novel and known microRNAs in small RNA deep‐sequencing data. Moreover, the usage of miRDeep2 to profile miRNA expression across samples is illustrated. Curr. Protoc. Bioinform. 36:12.10.1‐12.10.15. © 2011 by John Wiley & Sons, Inc.

Keywords: miRDeep2; miRNA; microRNA; gene prediction; sequencing; expression; profiling

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Table of Contents

  • Introduction
  • Basic Protocol 1: Using the Mapper Module to Preprocess and Map Raw Illumina Deep Sequencing Data
  • Basic Protocol 2: Using the Quantifier Module to Profile miRNA Expression Across Distinct Samples
  • Basic Protocol 3: Using the miRDeep2 Module to Identify Novel and Known miRNAs in Deep‐Sequencing Data
  • Support Protocol 1: Installing the miRDeep2 Package
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

   Bonnet, E., Wuyts, J., Rouze, 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.
   Friedländer, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., and Rajewsky, N. 2008. Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol. 26:407‐415.
   Friedländer, M.R., Mackowiak, S.D., Li, N., Chen, W., and Rajewsky, N. 2011. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. [Epub ahead of print]
   Griffiths‐Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., and Bateman, A. 2005. Rfam: Annotating non‐coding RNAs in complete genomes. Nucleic Acids Res. 33:D121‐D124.
   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.
   Hackenberg, M., Sturm, M., Langenberger, D., Falcon‐Perez, J.M., and Aransay, A.M. 2009. miRanalyzer: A microRNA detection and analysis tool for next‐generation sequencing experiments. Nucleic Acids Res. 37:W68‐W76.
   Hendrix, D., Levine, M., and Shi, W. 2010. miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol. 11:R39.
   Hofacker, I.L. 2003. Vienna RNA secondary structure server. Nucleic Acids Res. 31:3429‐3431.
   Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, D. 2002. The human genome browser at UCSC. Genome Res. 12:996‐1006.
   Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. 2009. Ultrafast and memory‐efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
   Lee, R.C., Feinbaum, R.L., and Ambros, V. 1993. The C. elegans heterochronic gene lin‐4 encodes small RNAs with antisense complementarity to lin‐14. Cell 75:843‐854.
   Mathelier, A. and Carbone, A. 2010. MIReNA: Finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics 26:2226‐2234.
   Winter, J., Jung, S., Keller, S., Gregory, R.I., and Diederichs, S. 2009. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat. Cell Biol. 11:228‐234.
Key References
   Friedländer et al., 2008. See above.
  Describes the first version of the software package with information of how the algorithm works in detail.
Internet Resources
  Site at which the miRDeep2 software can be downloaded.
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