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New Insights about the RNA Degradome with Agricultural Applications

Research from Academia Sinica’s Agricultural Biotechnology Research Center reveals a link between exon junction complexes on RNA and nonsense-mediated mRNA decay, with applications in agriculture.

While several aspects of molecular biology are well understood, there is still much to uncover about gene expression, particularly regarding RNA expression and degradation. A new study led by Dr. Chen Ho-Ming from the Agricultural Biotechnology Research Center of Academia Sinica investigated novel approaches for the analysis of RNA degradome data.

The RNA degradome refers to the collection of partially degraded mRNA molecules. This study, which was published in The Plant Cell in April this year, focuses on exon junction complexes (EJCs) on mRNAs. In turn, nonsense-mediated mRNA decay (NMD) recognises and degrades EJC-bound mRNA. The team found that EJCs form complexes with RNA during RNA synthesis and maturation but are removed when ribosomes bind to mRNA during translation. EJC can therefore be used to mark RNA for degradation before steady-state translation.

The researchers studied this interaction in the cells of four organisms: Arabidopsis (Arabodopsis thaliana, also known as the thale cress), rice (Oryza sativa), the model organism worm Caenorhabditis elegans, and humans (Homo sapiens). They observed that changes in the EJC footprint in organisms resulted in changes in gene expression, and that EJC footprints were most associated with NMD targets, suggesting that studying EJC footprints could provide information about RNA degradation through the NMD pathway.

This research has potential applications in agriculture, specifically crop defence mechanisms. Plants have natural antiviral RNA silencing pathways to protect them from infection by viruses, and RNA silencing pathways and technology have often been used to genetically modify crop plants to promote resistance to diseases and pests. Specifically, through these methods, scientists have been able to produce plants that are more resistant to biotic stresses such as viruses, bacteria, and fungi. The flowering time and architecture of plants can also be altered, so that plants’ appearances can be improved for ornamental plants and agriculture of crop plants can be optimised to growers’ needs. These methods also allow for the development of seedless fruits, and to boost the nutritional value of some crops, among several other important industrial and agricultural applications.

Besides the new findings of this study, other pathways of RNA silencing in plants include regulation by the miRNA pathway, the trans-acting siRNA pathway, and the RNA-directed DNA methylation pathway. Researchers take advantage of these pathways by employing transgenes of hairpin RNA, artificial constructs of miRNA or siRNA, or other transgenes specific for each RNA silencing pathway. Common foods available today have benefitted from these methods, including transgenic tomatoes with extended shelf lives, decaffeinated coffee beans, and transgenic potatoes whose nutritional content is boosted.

By gaining more understanding of gene expression mechanisms and the dynamics of RNA production and degradation, scientists could develop new methods for crop improvement. Such methods have been greatly beneficial to our development of modern crops and have contributed to the existence of many foods available to us today. The findings of Dr. Chen’s research group could lead to improved agricultural methods, higher yield and food availability, and greater nutritional value of harvested crops. [APBN]