In plants, the identification of mRNA targets is straight forward because most miRNAs and their target mRNAs have exact or nearly exact complementarity. In animals, the tendency of miRNAs to bind their mRNA targets with imperfect sequence homology poses considerable challenges with target prediction. Several computational approaches have been developed to facilitate experimental design and predicting miRNA targets. In general, computational target prediction identifies potential binding sites according to base-pairing rules and cross species conservation conditions.

miRNA target search databases

  • miRBase Sanger Institute miRNA databases of sequences and predicted targets, as well as an official name registry for new miRNA genes.
  • EumiR - searchable website for the prediction of microRNA precursor sequences hosted by the Institute of Genomics and Integrative Biology
  • miRanda - created by the Computational Biology Center of Memorial Sloan-Kettering Cancer Center
  • miRex - searchable website for the identification of microRNA targets hosted by the Rajewsky lab at NYU's Center for Comparative Functional Genomics
  • PicTar - searchable website for the identification of microRNA targets hosted by the Rajewsky lab at NYU's Center for Comparative Functional Genomics
  • TargetScanS - searchable website for the identification of microRNA targets hosted by the Whitehead Institute for Biomedical Research.

Interesting Target Prediction Review Articles

Sethupathy, P., et. al. A Guide Through Present Computational Approaches for the Identification of Mammalian microRNA Targets. Nature Methods.  2006: 3(11): 881-886.

Zhang, B., et. al. Computational Identification of microRNAs and Their Targets. Computational Biology and Chemistry. 2006; 30(6): 395-407.

Grittith-Jones, S. et al. miRBase: microRNA Sequences, Targets and Gene Nomenclature. Nucleic Acids Research. 2006: 34: 140-144. 

miRNA Target Validation

Several in vitro methods have proven useful to validate miRNA function, including RNA interference and protein analysis using SILAC.

Over-expression and knockdown functional studies  - Over-expression and knockdown of the expression of a specific miRNA in a cell has proven useful to elucidate miRNA function. There are three basic approaches to induce RNA interference: synthetic RNAi and siRNA duplexes, vectors carrying an RNAi cassette expressing shRNA or artificial miRNAs, and in vitro transcription and dicing of dsRNA to generate pools of siRNA.

Related RNA interference topics:

SILAC studies - Although miRNA profiling can show changes based on miRNA activity, it is not always indicative of translation inhibition. Protein analysis examining by mass spectrometry combined with stable isotopic labeling by amino acids in cell culture (SILAC) has shown a strong correlation with miRNA activity. This method relies upon the metabolic incorporation of 'light' or 'heavy' form of the amino acid into the proteins to distinguish differences between cell populations - such as normal and malignant breast tissue.

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