The decapping scavenger enzyme DCS-1: a new modulator of miRNA turnover.

MicroRNAs are small non-coding RNA able to silence posttranscriptionally gene expression of targeted mRNAs through partial base-pairing interactions. Found in nearly all eukaryotes (with the notable exception of yeast), microRNA-mediated gene regulation is involved in almost all biological processes. In recent years, many studies have described a correlation between changes in microRNA levels and several human pathologies. Different mechanisms have been proposed to control expression and maturation of microRNAs, and a number of cellular factors have been implicated in the regulation of microRNA biogenesis mainly by modulating activity of the processing complexes. More recently, the contribution of some ribonucleases in the degradation of microRNA molecules has been suggested in plant (SDNs), Caenorhabditis elegans (XRN-1 and XRN-2), and human cells (XRN-1, PNPase, and RRP41). However, it is still unclear how the stability and the fate of mature microRNAs can be affected in cells.

Using a genetic screen in Caenorhabdits elegans designed to identify new players important for the microRNA pathway, we uncovered the decapping scavenger enzyme DCS-1 (known as DcpS in mammals) as an important new actor in the microRNA turnover in animals. We observed that genetic alterations of the dcs-1 gene lead to a population of animals carrying adult traits (i.e., alae structure) one developmental stage earlier than wild-type worms. Since similar developmentally precocious phenotypes can be associated to a mis-regulation of the let-7 microRNA function, we therefore investigated the level and the activity of microRNAs in the dcs-1 mutant. We observed that the level of nearly 20% of the mature microRNA population, including let-7, was significantly increased in dcs-1 mutants. As opposed to other known factors implicated in microRNA regulation, such as LIN-28, the levels of primary and precursor intermediate microRNA molecules were not changed, suggesting that DCS-1 is a negative regulator of mature microRNAs stability. We also observed that the accumulation of microRNAs lead to a decrease of a let-7 target lin-41, demonstrating that DCS-1 was not acting through its bona fide decapping scavenger activity implicated in one of the major mRNA degradation pathways. Furthermore, using a mutant animal strain expressing a low level of mature let-7 microRNA at a non-permissive temperature, causing animal lethality, we were able to demonstrate that the loss of dcs-1 led to the accumulation of functional microRNAs.

In vitro degradation assays using whole worm extracts further support that DCS-1 is required for 5′–3′ degradation of microRNAs that are released from the microRNA-induced silencing complex (miRISC) in animals. Since microRNAs do not carry a cap structure at their 5′ end, nor does the DCS-1 protein have any exonuclease activity, we searched for exonucleases that could be controlled by DCS-1. As the 5′-3′ exonuclease XRN-1 was recently reported as a modulator of microRNAs in animals, we therefore tested the contribution of this exonuclease for dcs-1-dependent microRNA turnover. We observed that the DCS-1 immunopurified complex required XRN-1 to degrade microRNAs, and that the DCS-1 and XRN-1 proteins interact together, as recently observed in yeast. More importantly, we observed that DCS-1 is part of a microRNA degradation complex with XRN-1 that is independent of its decapping scavenger activity, uncovering a new role for DCS-1 in microRNA turnover.

Even if our study demonstrated a new function for the decapping scavenger enzyme DCS-1 in microRNAs turnover, thus providing important insights on this regulatory mechanism, interesting aspects of this new pathway remain to be discovered. One intriguing observation is that the stability of only a subset of microRNAs is dependent of dcs-1. While the expression of the dcs-1 gene appears to be regulated during animal development, suggesting that DCS-1 might contribute to a “burst” microRNA degradation during specific developmental cues (see Fig. 1), further analyses will be required to confirm the implication of the modulatory expression of dcs-1 in the turnover of specific microRNAs. A detailed characterization of how XRN-1 exonuclease activity is stimulated by DCS-1 could help to explain this unexpected specificity. In addition to this, it is still unclear what triggers the release of microRNAs from the miRISC in order to drive their degradation by the DCS-1/XRN-1 complex. Recent reports suggest that the base-pairing interaction between microRNAs and their mRNA targets can influence the stability of microRNAs in cells. It is therefore conceivable that the nature of the interaction between specific microRNAs with their targets contributes to their release from the miRISC and thus renders such microRNAs accessible for degradation by the DCS-1/XRN-1 complex. Further studies aiming to understand how microRNAs are released from the silencing complex will likely contribute to the discovery of how the specificity of microRNA turnover occurs in animals.

Figure 1. Schematic representation of miRNAs (blue) and DCS-1 (red) oscillating expression during animal development. DCS-1 regulation could also be involved in other biological context in which the levels of miRNAs need to be drastically changed (i.e., cellular stress, immune response).

In upcoming years it will be interesting to determine whether the DCS-1/XRN-1 complex can also contribute to microRNA turnover in human and other animal species. Knowing that many studies demonstrate deregulation of microRNA levels in several cancers, it is tempting to speculate that the DcpS-dependent microRNA degradation will play an important role in cancer formation and maintenance. Future studies will likely demonstrate the importance of precisely regulating microRNA stability through protein modulators such as DcpS for maintaining cell homeostasis.