Translation affects mRNA stability in a codon dependent manner in human cells
- Stowers Institute for Medical Research, United States
Abstract
mRNA translation decodes nucleotide into amino acid sequences. However, translation has also been shown to affect mRNA stability depending on codon composition in model organisms, although universality of this mechanism remains unclear. Here, using three independent approaches to measure exogenous and endogenous mRNA decay, we define which codons are associated with stable or unstable mRNAs in human cells. We demonstrate that the regulatory information affecting mRNA stability is encoded in codons and not in nucleotides. Stabilizing codons tend to be associated with higher tRNA levels and higher charged/total tRNA ratios. While mRNAs enriched in destabilizing codons tend to possess shorter poly(A)-tails, the poly(A)-tail is not required for the codon-mediated mRNA stability. This mechanism depends on translation; however, the number of ribosome loads into a mRNA modulates the codon-mediated effects on gene expression. This work provides definitive evidence that translation strongly affects mRNA stability in a codon-dependent manner in human cells.
Data availability
The following datasets have been uploaded to NCBI GSE, under the accession number GSE126523.Endogenous mRNA decay:1.293T: 0h, 0h, 1h, 2h,3h,6h,6h2.Hela: 0h,0h,1h,2h,3h,4h,5h,6h,6h3.RPE: 0h,0h,1h,2h,3h,4h,5h,6h,6hORFome:1.293t: 0h, 0h, 1h, 1h, 2h, 2h, 3h, 3h, 4h, 4h, 5h, 5h, 6h, 6h2.K562: 0h, 0h, 1h, 1h, 2h, 2h, 3h, 3h, 4h, 4h, 5h, 5h, 6h, 6hSLAM-seq:1.K562: 0h, 0h, 0h, 2h, 2h, 2h, 4h, 4h, 4h, 6h, 6h, 6h
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HSV1 infection dataNCBI Gene Expression Omnibus, GSE59717.
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hydro- tRNA seq, table S1NCBI Gene Expression Omnibus,GSE95683.
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TGIRT tRNA seq and charged ratioNCBI Gene Expression Omnibus, GSE97259.
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TAIL-seq helaNCBI Gene Expression Omnibus, GSE54114.
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PAL-seq 293TNCBI Gene Expression Omnibus, GSE52809.
Article and author information
Author details
Ariel Alejandro Bazzini
Funding
Stowers Institute for Medical Research
- Ariel Alejandro Bazzini
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Nahum Sonenberg, McGill University, Canada
Ethics
Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the zebrafish were handled according to approved institutional animal care and use committee (IACUC) protocols (#2016-0159) of the Stowers Institute for Medical Research. The protocol was approved on August 18th 2018.
Version history
- Received: January 21, 2019
- Accepted: April 20, 2019
- Accepted Manuscript published: April 23, 2019 (version 1)
- Version of Record published: May 21, 2019 (version 2)
Copyright
© 2019, Wu 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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Translation affects mRNA stability in a codon dependent manner in human cells
eLife 8:e45396.
https://doi.org/10.7554/eLife.45396
Further reading
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- Biochemistry and Chemical Biology
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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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