Mol. Cell https://doi.org/10.1016/j.molcel.2019.05.008 (2019)
Transcripts carrying nonsense mutations undergo rapid degradation via nonsense-mediated mRNA decay (NMD) to prevent accumulation of toxic truncated peptides. Previous studies have shown that mRNA molecules with different sequences exhibit NMD with varying efficiency, but a lack of useful detection methods makes it challenging to reveal the underlying mechanisms. To precisely determine the cleavage kinetics of NMD, Hoek et al. developed a method to visualize the translation and degradation of single mRNA molecules carrying premature termination codons (PTCs) in live cells. They introduced fluorescent tags at the 5′ and 3′ ends of a reporter transcript and observed the exact moment of NMD cleavage for each molecule, as this resulted in separation of the two fluorescence signals. Using this system, they found that the cleavage rate was affected by exon sequences downstream of the PTC, the distance of the PTC to downstream introns, and the number of introns. In addition, they uncovered the kinetics by which XRN1 degrades the 3′ cleavage fragments produced by NMD. This study provides a useful tool to investigate the kinetics of RNA degradation and deepens our mechanistic understanding of NMD.