Abstract
Nonsense-mediated mRNA decay (NMD) is a well-known eukaryotic surveillance mechanism that eliminates aberrant mRNAs that contain a premature termination codon (PTC). UP-Frameshift (UPF) proteins, UPF1 and UPF3, are essential for normal NMD function. Here, we noticed that, in Arabidopsis, most of the mRNA-like noncoding RNAs (mlncRNAs) have the features of NMD substrate. We examined transcriptomes of two Arabidopsis mutants, upf1-1 and upf3-1, using whole genome tiling arrays. The results expectedly showed that many mlncRNAs were upregulated in both mutants. Thus, it is indicated that mlncRNAs are targeted by NMD system.
The 5'-to-3' RNA degradation by NMD is mediated by an exonuclease, XRN1, in animals. Arabidopsis has three genes encoding XRN enzymes. We examined expression profiles of three mutants, xrn2, xrn3 and xrn4, using tiling arrays. However, significant upregulation of mlncRNAs was not detected in all mutants. A previous report suggested that FRY1 protein promotes XRN activity. Increased accumulation of some mlncRNAs was detected in fry1 mutants. Thus, these results imply that three XRNs redundantly act on degradation of NMD-targeted RNAs.
