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Predicting microRNA targets and functions: traps for the unwary

Nature Methods volume 6, pages 397–398 (2009)Cite this article

To the Editor: microRNAs (miRNAs) are short RNAs that are important in gene regulation in many organisms. In mammals, they guide the RNA-induced silencing complex to target sites typically located in the 3′ untranslated regions (UTR) of mRNAs, causing translational repression and/or mRNA degradation1. Despite recent advances in large-scale target screening techniques, experimental validation of miRNA targets remains cumbersome, and computational approaches remain the most commonly used method to identify putative target genes.

Most algorithms use sequences collected from either the Ensembl2 or University of California Santa Cruz (UCSC)3 databases and then preprocess these sequences to correct for genes that do not have a predicted 3′ UTR of sufficient length. However, these databases use different criteria to define 3′ UTR boundaries (Supplementary Fig. 1 online) and these boundaries will change as more sequences from varied tissue types are added to them4.

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Acknowledgements

Financial support was provided by the Australian National Health and Medical Research Council (project grant 402730, Training Fellowship 571156), the Rebecca L Cooper Foundation and the Cell and Gene Trust.

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Authors and Affiliations

  1. Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Sydney, Australia

    William Ritchie, Stephane Flamant & John E J Rasko

  2. Cell and Molecular Therapies, Sydney Cancer Centre, Royal Prince Alfred Hospital, Camperdown, Australia

    John E J Rasko

Authors
  1. William Ritchie
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  2. Stephane Flamant
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  3. John E J Rasko
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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6, Supplementary Tables 1–2, Supplementary Data, Supplementary Methods (PDF 681 kb)

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Ritchie, W., Flamant, S. & Rasko, J. Predicting microRNA targets and functions: traps for the unwary. Nat Methods 6, 397–398 (2009). https://doi.org/10.1038/nmeth0609-397

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