Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability
- University of California, Berkeley, United States
- ETH Zurich, Switzerland
Abstract
The cytoplasmic abundance of mRNAs is strictly controlled through a balance of production and degradation. Whereas the control of mRNA synthesis through transcription has been well characterized, less is known about the regulation of mRNA turnover, and a consensus model explaining the wide variations in mRNA decay rates remains elusive. Here, we combine non-invasive transcriptome-wide mRNA production and stability measurements with selective and acute perturbations to demonstrate that mRNA degradation is tightly coupled to the regulation of translation, and that a competition between translation initiation and mRNA decay -but not codon optimality or elongation- is the major determinant of mRNA stability in yeast. Our refined measurements also reveal a remarkably dynamic transcriptome with an average mRNA half-life of only 4.8 minutes - much shorter than previously thought. Furthermore, global mRNA destabilization by inhibition of translation initiation induces a dose-dependent formation of processing bodies in which mRNAs can decay over time.
Data availability
Sequencing data have been deposited in GEO under accession code GSE119560.
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mRNA stability as measured by thiouracil incorporation in the presence and absence of translational inhibitorsublicly available at the NCBI Gene Expression Omnibus (accession no: GSE119560).
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translational efficiencyGEO accession number: GSE34082.
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Cramer (2) mRNA halflifePublicly available.
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Peltz mRNA halflifeSupplementary Tables S1, S2, and S3 (Publicly available).
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Coller (1) and (2) mRNA halflifeTable S1 (Publicly available).
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Struhl mRNA stabilityTable S2 (Publicly available).
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Pipel mRNA stabilitySupplementary Table 1 (Publicly available).
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Weis (1) mRNA stabilitySupplemental Data (Publicly available).
Article and author information
Author details
Christopher F Mugler
Stephanie Heinrich
Funding
National Institutes of Health
- Leon Y Chan
- Christopher F Mugler
- Karsten Weis
Damon Runyon Cancer Research Foundation
- Leon Y Chan
Shurl and Kay Curci Foundation
- Leon Y Chan
European Molecular Biology Organization
- Stephanie Heinrich
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Stephanie Heinrich
- Pascal Vallotton
- Karsten Weis
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Alan G Hinnebusch, National Institutes of Health, United States
Version history
- Received: October 6, 2017
- Accepted: August 13, 2018
- Accepted Manuscript published: September 7, 2018 (version 1)
- Version of Record published: September 24, 2018 (version 2)
- Version of Record updated: October 3, 2018 (version 3)
- Version of Record updated: February 1, 2019 (version 4)
Copyright
© 2018, Chan et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability
eLife 7:e32536.
https://doi.org/10.7554/eLife.32536
Further reading
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- Biochemistry and Chemical Biology
- Chromosomes and Gene Expression
Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.
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- Chromosomes and Gene Expression
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