Journal Club: Target Mimicry as a New Way to Regulate microRNA Activity

Just how intricately RNAi-related pathways can be wired, is demonstrated by a study on the fate a nutrient-regulated microRNA in plants [Franco-Zorrilla et al. (2007). Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genetics, Advance Online Publication, doi: 10.1038/ng2079].

Unlike in animals where microRNAs recognise targets sites of incomplete base-pair complementarity to promote translational repression, microRNAs in plants largely target fully complementary sites in an mRNA. Like with perfectly paired siRNAs in animals, this leads to the destruction of the targeted transcript by endonucleolytic cleavage at the target site. This process is thought to be rapid and the small RNA is then free to recycle and target a new message. By contrast, the turnover rate for animal microRNAs is much less well understood. However, as was often the case in the relatively short history of RNAi-related research, this study in plants may offer us a clue about the kinetics of microRNA activity in animals.

Franco-Zorrilla and colleagues observe that the induction of a microRNA that is regulated based on phosphate availability and that has known target transcripts based on perfect microRNA-target site complementarities around the expected cleavage sites, is accompanied by another non-coding RNA (RNA that is not translated into proteins) that also has high base-pair complementarity to the microRNA, but with telling mismatches around the otherwise predicted cleavage site. Sure enough, this non-coding RNA is recognised by the microRNA, but not degraded. Through a series of elegant genetics, the authors demonstrate that this sufficiently diverts the microRNA, which is of low abundance to start with, so that it cannot act on their “normal” mRNA substrates any more. Hence, the non-coding RNA functions as a sink and regulates microRNA activity by tricking it to bind to itself. This strongly suggests that the turnover of the microRNA complex on incompletely based-paired targets is very slow and suppression requires a one-to-one microRNA-target site relationship.

If you have cared to read all this, I will now tell you what I think the implications are for the development of RNAi Therapeutics. When thinking about off-target effects, we have been largely concerned about the detrimental effects of suppressing unintended mRNAs, largely through microRNA-like translational suppression. However, if the plant system reflects RNA silencing kinetics in humans, then another consequence of off-targeting may be decreased on-target activity due to decreasing the pool of available siRNAs. Consequently, if it were possible to prevent such off-targeting, for example through chemical modifications and bioinformatics, then one could think about lower siRNA doses in the clinic. It is not clear whether the 2’O-methylation strategy pioneered by Dharmacon scientists to limit off-target silencing also prevents microRNA-like binding of an siRNA to incompletely based-paired RNAs, but the strategy certainly points in the right direction.