Current tools for the identification of miRNA genes and their targets

Abstract

The discovery of microRNAs (miRNAs), almost 10 years ago, changed dramatically our perspective on eukaryotic gene expression regulation. However, the broad and important functions of these regulators are only now becoming apparent. The expansion of our catalogue of miRNA genes and the identification of the genes they regulate owe much to the development of sophisticated computational tools that have helped either to focus or interpret experimental assays. In this article, we review the methods for miRNA gene finding and target identification that have been proposed in the last few years. We identify some problems that current approaches have not yet been able to overcome and we offer some perspectives on the next generation of computational methods.

Figure 1.

The miRNA biogenesis in metazoans. The figure shows two major pathways for metazoan miRNA biogenesis. The pri-miRNA is indicated as a polycistronic transcript. The stem–loops are cleaved by Drosha in the nucleus giving rise to the pre-miRNA. Alternatively, the pre-miRNA can originate from a particular kind of intron—the mirtron. The pre-miRNA is shown with a red strand (the mature miRNA) and a yellow strand (the miRNA*). The pre-miRNA is then exported by Exp5 and processed by Dicer in the cytosol. The red strand of the resulting duplex is integrated in the miRISC and the yellow strand is degraded. Depending on the degree of complementarity to the target site, the silencing complex will either cleave the mRNA inducing immediate degradation or promote translational attenuation. The mechanism of translational attenuation can also subsequently promote target degradation.