Biochimica et Biophysica Acta 2013 / 12 Vol. 1829; Iss. 12
Gene silencing in plants: A diversity of pathways
Angel Emilio Martínez de Alba, Emilie Elvira-Matelot, Hervé Vaucheret


Eukaryotic organisms have evolved a variety of gene silencing pathways in which small RNAs, 20- to 30-nucleotides in length, repress the expression of sequence homologous genes at the transcriptional or post-transcriptional levels. In plants, RNA silencing pathways play important roles in regulating development and response to both biotic and abiotic stresses. The molecular basis of these complex and interconnected pathways has emerged only in recent years with the identification of many of the genes necessary for the biogenesis and action of small RNAs. This review covers the diversity of RNA silencing pathways identified in plants.

5. Conclusions

The existence of multiple silencing pathways reflects the diversity of targets that plants have to control during development and stress response, and their absolute need to adapt to challenging environment because of their sessile nature. Remarkably, most of the components of the diverse plant RNA silencing pathways have been identified during genetic screens based on the reactivation of various transgenes subjected to either TGS or PTGS. Indeed, most plant mutants impaired in RNA silencing develop normally and could not have been recovered in genetic screens based on an alteration of development, with the exception of mutants impaired in the miRNA and trans-acting siRNAs (ta-siRNA) pathways, which exhibit obvious developmental defects. Therefore, genetic screens based on the reactivation of transgenes subjected to TGS or PTGS have been and are still instrumental for the identification of endogenous small RNA pathways and their actors or counter-actors. The recent development of high-throughput sequencing techniques, allowing a rapid determination of mutations, promises the identification of many more components of RNA silencing pathways in the near future. Likely, the combination of genetic screens and biochemical approaches, which allow identifying partners that are essential for the plant's life or that are encoded by multi-gene families, will soon reveal the full set of RNA silencing components.

The elucidation of the full RNA silencing-machinery will be essential to understand the many aspects of RNA silencing that remain mysterious. For example, it is still not known how RNA silencing propagates systemically from cell-to-cell (short-distance signaling) and through the vasculature (long-distance signaling) [140–144]. It also remains unclear what enables some small RNAs to move and others to remain in the originating cell. Answering these questions is essential to achieve reliable and controlled silencing when trying to knockdown endogenous genes using transgenes.

The specificity of RNA silencing mechanisms towards exogenous versus endogenous sequences also is a fundamental question, as well as understanding why a given locus has the capacity to acquire and inherit epigenetic modifications. Indeed, TGS correlates with chromatin modifications, which sometimes are inherited, thus maintaining silencing over multiple generations, even after the initial trigger has been eliminated. However, whereas transgene TGS is commonly inherited, TGS of endogenous genes is rarely inherited [145]. PTGS also correlates with DNA and histone methylation. However, these marks only are found on transgenes, but not on endogenous genes subjected to PTGS. Together, these results suggest that cells are able to distinguish transgenes form endogenous genes, a process that may be linked to the establishment of specific chromatin marks on de novo introduced DNA [146].