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.
-
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).
-
translational efficiencyGEO accession number: GSE34082.
-
Cramer (2) mRNA halflifePublicly available.
-
Peltz mRNA halflifeSupplementary Tables S1, S2, and S3 (Publicly available).
-
Coller (1) and (2) mRNA halflifeTable S1 (Publicly available).
-
Struhl mRNA stabilityTable S2 (Publicly available).
-
Pipel mRNA stabilitySupplementary Table 1 (Publicly available).
-
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.
Metrics
-
- 26,797
- views
-
- 2,268
- downloads
-
- 116
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
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
-
- Chromosomes and Gene Expression
Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription-site-proximal zone through which RNA move more slowly than in the nucleoplasm. Full-length pre-mRNA undergo continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.
-
- Chromosomes and Gene Expression
- Genetics and Genomics
Heterogeneity in endothelial cell (EC) sub-phenotypes is becoming increasingly appreciated in atherosclerosis progression. Still, studies quantifying EC heterogeneity across whole transcriptomes and epigenomes in both in vitro and in vivo models are lacking. Multiomic profiling concurrently measuring transcriptomes and accessible chromatin in the same single cells was performed on six distinct primary cultures of human aortic ECs (HAECs) exposed to activating environments characteristic of the atherosclerotic microenvironment in vitro. Meta-analysis of single-cell transcriptomes across 17 human ex vivo arterial specimens was performed and two computational approaches quantitatively evaluated the similarity in molecular profiles between heterogeneous in vitro and ex vivo cell profiles. HAEC cultures were reproducibly populated by four major clusters with distinct pathway enrichment profiles and modest heterogeneous responses: EC1-angiogenic, EC2-proliferative, EC3-activated/mesenchymal-like, and EC4-mesenchymal. Quantitative comparisons between in vitro and ex vivo transcriptomes confirmed EC1 and EC2 as most canonically EC-like, and EC4 as most mesenchymal with minimal effects elicited by siERG and IL1B. Lastly, accessible chromatin regions unique to EC2 and EC4 were most enriched for coronary artery disease (CAD)-associated single-nucleotide polymorphisms from Genome Wide Association Studies (GWAS), suggesting that these cell phenotypes harbor CAD-modulating mechanisms. Primary EC cultures contain markedly heterogeneous cell subtypes defined by their molecular profiles. Surprisingly, the perturbations used here only modestly shifted cells between subpopulations, suggesting relatively stable molecular phenotypes in culture. Identifying consistently heterogeneous EC subpopulations between in vitro and ex vivo models should pave the way for improving in vitro systems while enabling the mechanisms governing heterogeneous cell state decisions.
