Single-Molecule Imaging Uncovers Rules Governing Nonsense-Mediated mRNA Decay

Tim A Hoek, Deepak Khuperkar, Rik G H Lindeboom, Stijn Sonneveld, Bram M P Verhagen, Sanne Boersma, Michiel Vermeulen, Marvin E Tanenbaum

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Abstract

Nonsense-mediated decay (NMD) is a surveillance system that degrades mRNAs containing a premature termination codon (PTC) and plays important roles in protein homeostasis and disease. The efficiency of NMD is variable, impacting the clinical outcome of genetic mutations. However, limited resolution of bulk analyses has hampered the study of NMD efficiency. Here, we develop an assay to visualize NMD of individual mRNA molecules in real time. We find that NMD occurs with equal probability during each round of translation of an mRNA molecule. However, this probability is variable and depends on the exon sequence downstream of the PTC, the PTC-to-intron distance, and the number of introns both upstream and downstream of the PTC. Additionally, a subpopulation of mRNAs can escape NMD, further contributing to variation in NMD efficiency. Our study uncovers real-time dynamics of NMD, reveals key mechanisms that influence NMD efficiency, and provides a powerful method to study NMD.

Original languageEnglish
Pages (from-to)324-339.e11
JournalMolecular Cell
Volume75
Issue number2
DOIs
Publication statusPublished - 25 Jul 2019

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    Hoek, T. A., Khuperkar, D., Lindeboom, R. G. H., Sonneveld, S., Verhagen, B. M. P., Boersma, S., Vermeulen, M., & Tanenbaum, M. E. (2019). Single-Molecule Imaging Uncovers Rules Governing Nonsense-Mediated mRNA Decay. Molecular Cell, 75(2), 324-339.e11. https://doi.org/10.1016/j.molcel.2019.05.008