Despite the recent rapid progress in understanding the roles of microRNAs (miRNAs), it seems that we still have a lot to learn. Two recent studies of animal miRNAs not only reveal a new mode of action for these molecules, but also indicate that they might have a far wider regulatory role than was previously appreciated.

In animals, miRNAs are thought to regulate gene expression by inhibiting translation. Lee Lim and colleagues investigated whether, like their plant equivalents, animal miRNAs also trigger transcript degradation. They transfected human cells with two miRNA sequences and examined their effects on gene expression using microarrays. For both miRNAs, many transcripts were downregulated, indicating widespread effects at the mRNA level.

Is this transcript downregulation direct, or is it a secondary effect that is caused by decreased expression of regulatory genes? Using a computational method, the authors identified motifs that were over-represented in the 3′ untranslated regions of the downregulated transcripts. These motifs showed complementarity to 5′ regions of the miRNAs, indicating that downregulation is mediated by a direct interaction between the miRNAs and their target transcripts.

Further support for this conclusion came from examining the sets of transcripts that were downregulated by the two miRNAs, both of which have specific expression patterns in vivo. The transcripts they regulated in the microarray experiments correspond to genes that are expressed at lower levels in the tissues with the highest abundance of the miRNAs. This correlation between in vivo expression patterns and in vitro activities provides strong evidence that the results of the microarray analysis are biologically relevant.

In a second study, Benjamin Lewis and colleagues provide evidence that more than a third of human genes are regulated by miRNAs. The authors reasoned that, for genuine targets, sites of interaction with the regulatory miRNA would be preserved in orthologous genes from other vertebrates much more frequently than similarly abundant sites that lack complementarity to the miRNA. This requirement for conservation allowed them to refine other constraints in searches for potential target genes. In the gene set that was analysed by the authors, more than a third of the genes were identified as conserved miRNA targets, a much larger figure than previously estimated.

Our knowledge of the regulatory importance of miRNAs and their mechanisms of action is increasing all the time; the next challenge will be to assimilate this information to understand how miRNAs define specific patterns of gene expression.