Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis.
The nonsense-mediated mRNA decay (NMD) pathway is a well-known eukaryotic surveillance mechanism that eliminates aberrant mRNAs that contain a premature termination codon (PTC). The UP-Frameshift (UPF) proteins, UPF1, UPF2, and UPF3, are essential for normal NMD function. Several NMD substrates have been identified, but detailed information on NMD substrates is lacking. Here, we noticed that, in Arabidopsis, most of the mRNA-like nonprotein-coding RNAs (ncRNAs) have the features of an NMD substrate. We examined the expression profiles of 2 Arabidopsis mutants, upf1-1 and upf3-1, using a whole-genome tiling array. The results showed that expression of not only protein-coding transcripts but also many mRNA-like ncRNAs (mlncRNAs), including natural antisense transcript RNAs (nat-RNAs) transcribed from the opposite strands of the coding strands, were up-regulated in both mutants. The percentage of the up-regulated mlncRNAs to all expressed mlncRNAs was much higher than that of the up-regulated protein-coding transcripts to all expressed protein- coding transcripts. This finding demonstrates that one of the most important roles of NMD is the genome-wide suppression of the aberrant mlncRNAs including nat-RNAs.
Kurihara
Yukio
Y
Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan.
Matsui
Akihiro
A
Hanada
Kousuke
K
Kawashima
Makiko
M
Ishida
Junko
J
Morosawa
Taeko
T
Tanaka
Maho
M
Kaminuma
Eli
E
Mochizuki
Yoshiki
Y
Matsushima
Akihiro
A
Toyoda
Tetsuro
T
Shinozaki
Kazuo
K
Seki
Motoaki
M
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000378:metabolism; D003513:Cycloheximide / Q000494:pharmacology; D005091:Exons; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D008954:Models, Biological; D008957:Models, Genetic; D009154:Mutation; D011500:Protein Synthesis Inhibitors / Q000494:pharmacology; D012313:RNA / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
D029681:Arabidopsis Proteins; D011500:Protein Synthesis Inhibitors; D012333:RNA, Messenger; D022661:RNA, Untranslated; D012313:RNA; D003513:Cycloheximide