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Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis

Yukio Kurihara1, Akihiro Matsui, Kousuke Hanada

  • 1Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan.

Proceedings of the National Academy of Sciences of the United States of America
|February 3, 2009
PubMed

Insights

The nonsense-mediated mRNA decay (NMD) pathway suppresses aberrant non-coding RNAs in Arabidopsis. NMD targets many mRNA-like non-coding RNAs (mlncRNAs), including natural antisense RNAs, preventing their accumulation.

Area of Science:

  • Plant molecular biology
  • RNA biology
  • Gene regulation

Background:

  • The nonsense-mediated mRNA decay (NMD) pathway is a crucial eukaryotic surveillance mechanism.
  • NMD eliminates aberrant messenger RNAs (mRNAs) with premature termination codons (PTCs).
  • UP-Frameshift (UPF) proteins (UPF1, UPF2, UPF3) are essential for NMD function.

Purpose of the Study:

  • To investigate the role of NMD in regulating mRNA-like non-coding RNAs (mlncRNAs) in Arabidopsis.
  • To identify specific types of mlncRNAs regulated by NMD.

Main Methods:

  • Analysis of gene expression profiles in Arabidopsis mutants (upf1-1 and upf3-1) using whole-genome tiling arrays.
  • Comparison of expression levels of protein-coding transcripts and mlncRNAs in wild-type versus mutant plants.

Main Results:

  • Expression of both protein-coding transcripts and mlncRNAs was significantly upregulated in upf1-1 and upf3-1 mutants.
  • A higher proportion of expressed mlncRNAs were upregulated compared to protein-coding transcripts in the mutants.
  • Natural antisense transcript RNAs (nat-RNAs) were identified as a major class of upregulated mlncRNAs.

Conclusions:

  • NMD plays a critical role in the genome-wide suppression of aberrant mlncRNAs in Arabidopsis.
  • NMD is essential for controlling the expression levels of mlncRNAs, including nat-RNAs.
  • This study highlights a previously underappreciated function of NMD in non-coding RNA quality control.

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