Abstract
Messenger RNAs with premature stop codons (PTCs) are targeted by RNA quality control systems such as nonsense mediated mRNA decays (NMD). Several recent researches found that it is a common regulatory mechanism of RNA metabolism to generate alternatively spliced mRNAs with PTCs under certain regulation, which are followed by NMD. This mechanism is called RUST (Regulated Unproductive Splicing and Translation). For understanding complex systems of RNA metabolism, studying which genes are subjected by RUST is important. In this study, we developed a novel method to evaluate NMD effects on every intron based on tiling array results. We have performed 18 sets of tiling array experiments to take transcriptome of Arabidopsis thaliana for specific tissues, those under environmental stresses, and those on several developmental stages. We computationally analyzed them and listed introns which possibly retained in mature mRNAs in certain conditions. Besides, in several cases, the genes had small expression values in the conditions where the introns were retained. These results suggested that we successfully found introns which were affected by NMD and RUST.
