Title: RNA-Seq-based identification and analysis of uridine-to-cytidine RNA editing related genes in Arabidopsis thaliana

Biography:

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.

Abstract

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.