Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation
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Abstract
Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. They also indicate that emergent polypeptides with as few as three basic residues within a ten-residue window tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was less than previously reported, and most of this variation could be predicted with a simple model that considered mRNA abundance, upstream open reading frames, cap-proximal structure and nucleotide composition, and lengths of the coding and 5' UTRs. Collectively, our results provide a framework for executing and interpreting ribosome-profiling studies and reveal key features of translational control in yeast.
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A later yeast ribosome profiling study found only 15-fold variability among individual proteins in the 1st-99th percentile range (Weinberg et al., 2016).
“However, a more recent study on ribosomal profiling of yeast demonstrated only 15-fold variability among individual proteins in the 1 st -99 th percentile range (Weinberg et al., 2016).”
From Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast (2017) · cites this paper as Weinberg et al., 2016
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- Authors
- Weinberg, D. E., Shah, P., Eichhorn, S. W., Hussmann, J. A., Plotkin, J. B., & Bartel, D. P.
- Affiliations
- University of California, San Francisco (US)
- University of Pennsylvania (US)
- Howard Hughes Medical Institute (US)
- The University of Texas at Austin (US)
- Corresponding author
- Weinberg, David E.
- ORCID
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2016-02
- Volume
- 14
- Issue
- 7
- Pages
- 1787-1799
- ISSN
- 2211-1247 (ISSN-L)
- PMC
- PMC4767672
- OpenAlex
- W2793056129
- Cited by
- 392
- References
- 79
- Citations by year
- 2026: 11 · 2025: 32 · 2024: 41 · 2023: 38 · 2022: 25 · 2021: 51 · 2020: 45 · 2019: 42 · 2018: 38 · 2017: 41 · 2016: 26 · 2015: 2
- FWCI
- 25.46
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Burroughs Wellcome Fund
- U.S. Department of the Interior (D12AP00025)
- Army Research Office (W911NF-12-1-0552)
- Sandler Foundation
- University of California, San Francisco
- David and Lucile Packard Foundation
- National Institutes of Health (DP5OD017895, GM061835)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Keywords
- ribosome profiling, mRNA levels, Saccharomyces cerevisiae, translational regulation, codon usage, basic residues, upstream open reading frames, mRNA cap, gene expression quantification
- MeSH terms
- Codon, Ribosomes, RNA, Transfer, Saccharomyces cerevisiae, Protein Biosynthesis, Models, Statistical, Gene Expression Regulation, Fungal, Open Reading Frames, Genome, Fungal, 5' Untranslated Regions, Saccharomyces cerevisiae Proteins
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