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.
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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Gene regulation is essential for life and controlled by regulatory DNA. Mutations can modify the activity of regulatory DNA, and also create new regulatory DNA, a process called regulatory emergence. Non-regulatory and regulatory DNA contain motifs to which transcription factors may bind. In prokaryotes, gene expression requires a stretch of DNA called a promoter, which contains two motifs called –10 and –35 boxes. However, these motifs may occur in both promoters and non-promoter DNA in multiple copies. They have been implicated in some studies to improve promoter activity, and in others to repress it. Here, we ask whether the presence of such motifs in different genetic sequences influences promoter evolution and emergence. To understand whether and how promoter motifs influence promoter emergence and evolution, we start from 50 ‘promoter islands’, DNA sequences enriched with –10 and –35 boxes. We mutagenize these starting ‘parent’ sequences, and measure gene expression driven by 240,000 of the resulting mutants. We find that the probability that mutations create an active promoter varies more than 200-fold, and is not correlated with the number of promoter motifs. For parent sequences without promoter activity, mutations created over 1500 new –10 and –35 boxes at unique positions in the library, but only ~0.3% of these resulted in de-novo promoter activity. Only ~13% of all –10 and –35 boxes contribute to de-novo promoter activity. For parent sequences with promoter activity, mutations created new –10 and –35 boxes in 11 specific positions that partially overlap with preexisting ones to modulate expression. We also find that –10 and –35 boxes do not repress promoter activity. Overall, our work demonstrates how promoter motifs influence promoter emergence and evolution. It has implications for predicting and understanding regulatory evolution, de novo genes, and phenotypic evolution.
