Japan Advanced Institute of Science and Technology, Japan
Ruchika is currently pursuing her phD under Dr. Toshifumi Tsukahara in the Area of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, Japan.
Cytosine-to-Uridine (C-to-U) and adenine-to-inosine (A-to-I) RNA editing involves the deamination phenomenon, which is common in animals and plants; however, the amination of U-to-C is confined to the plants. In this study, the high-throughput RNA sequencing (RNA-seq) of 12-days-old Arabidopsis seedlings was performed, which enables transcriptome-wide identification of RNA editing sites to analyse differentially expressed genes (DEGs) and nucleotide base conversions. The results showed that DEGs were expressed to higher levels in 12-days-old seedlings than in 20-days-old seedlings. This was confirmed by higher higher Fragment Per Kilobase of transcript per Million mapped reads (FPKM) values, read counts, and more up-regulated genes, in 12-days-old seedlings. Additionally, pentatricopeptide repeat (PPR) genes were also expressed at higher levels as indicated by the log2FC values. The U-to-C RNA editing are predominantly found in the untranslated region (UTR) region of the mature mRNA and affect its secondary structure. Our results suggest that U-to-C RNA editing in mature transcripts impacts plant physiology. Furthermore, we investigated the physiological role of U-to-C RNA editing in Arabidopsis by using the transcription inhibitor, Actinomycin D (ActD). Addition of ActD to the cell suspension culture of transgenic Arabidopsis generated by Agrobacterium-mediated transformation revealed that single nucleotide conversion adversely affects the secondary structure and mRNA half-life of PPR protein.
- Plant Genome Science
- Agricultural Science
- Molecular Plant Breeding
- Stress Signalling in Plants
- Plant Proteomics and Plant Science
- Plant Morphology and Plant Metabolism
- Crop Improvement and Plant Virology
- Plant Nutritional Genomics
- Plant Biotechnology
- Medicinal and Aromatic Plant Sciences
- Plants and Climate Change- Overcoming Measures