Roles of No-go RNA decay in the initiation of epigenetic silencing

Most living organisms carry DNA called transposable elements (TEs or transposons), which were once foreign to organisms but are now part of their DNA. These TEs originally came from ancient viruses and are best known for their ability to move their genomic locations and thereby cause gene mutations. In some crop plants, they can make up about 90% of the total DNA, and thus pose a greater threat to plant DNA stability and consequently crop production. Because of their mutagenic nature, they are tightly controlled by the host through the so-called epigenetic silencing mechanisms. These involve DNA methylation and heterochromatin formation, which are primarily guided by small interfering RNAs (siRNAs). In plants, there are two types of siRNAs: longer siRNAs of 24 nucleotides that are generated at already methylated DNAs and act to further reinforce the silent state (a process of which is called RNA-directed DNA methylation, in short RdDM), and shorter siRNAs of 21 and 22 nucleotides that establish new DNA methylation at naïve and active TEs. Intriguingly, these shorter siRNAs are produced exclusively by TEs and not by regular genes, however, the mechanisms underlying its selective action towards non-native DNA remain largely unknown. Therefore, this research project aims at unveiling the plant’s strategy to detect foreign DNA and initiate the epigenetic silencing, preventing them from damaging the host genomes. We previously found that TE RNAs are weak in translation, which can then lead to RNA localisation to cytoplasmic compartments known as stress granules, where the siRNA biogenesis pathway exists. Of note, reduced translation is frequently associated with RNA cleavage, which is a critical requirement for the siRNA biogenesis factors to act upon. However, the cellular mechanism linking translational inefficiency and entrance to the siRNA biogenesis pathway has been entirely unknown. To fill this gap, we paid attention to the No-go RNA decay (NGD) pathway, an under-investigated RNA quality control system in plants, which senses the stalled ribosome and triggers RNA cleavage. Importantly, our pilot experiments revealed that the key NGD components are localised in stress granules, and the loss of NGD results in compromised siRNA production. Through this project, we aim to further dissect the role of NGD in the initiation of epigenetic silencing in Arabidopsis, by 1) investigating the physical association of NGD with RdDM, 2) profiling the siRNA and RNA cleavage landscapes in the NGD mutants, and 3) characterising the direct RNA targets of NGD. Understanding the initiation of epigenetic silencing can have broader impact beyond transposon control and genome surveillance; for example, the shorter type of siRNAs (21 and 22 nucleotides) can be generated when plant cells are infected by viruses and express foreign transgenes. This implies that the plant siRNA-mediated epigenetic silencing pathway is an innate defence mechanism of the host against non-native DNA. Therefore, this research project will help improve antiviral treatments for plants and innovate the plant synthetic biology platforms. Overall, this work is relevant to the BBSRC research priority in “understanding the rules of life” as well as this year's BBSRC spotlight in “plant health”.