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Precision and functional specificity in mRNA decay
Yulei Wang1, Chih Long Liu, John D Storey
1Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.
Abstract:
Posttranscriptional processing of mRNA is an integral component of the gene expression program. By using DNA microarrays, we precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II. The half-lives varied widely, ranging from approximately 3 min to more than 90 min. We found no simple correlation between mRNA half-lives and ORF size, codon bias, ribosome density, or abundance. However, the decay rates of mRNAs encoding groups of proteins that act together in stoichiometric complexes were generally closely matched, and other evidence pointed to a more general relationship between physiological function and mRNA turnover rates. The results provide strong evidence that precise control of the decay of each mRNA is a fundamental feature of the gene expression program in yeast.
Insights
Yeast mRNA decay rates vary significantly, with no simple correlation to mRNA features. However, decay rates often match for mRNAs in protein complexes, suggesting functional regulation of gene expression.
Area of Science:
- Molecular Biology
- Yeast Genetics
- Gene Expression Regulation
Background:
- Posttranscriptional processing of messenger RNA (mRNA) is crucial for gene expression.
- Understanding mRNA stability is key to deciphering cellular regulation.
Purpose of the Study:
- To precisely measure the decay rates of individual yeast mRNAs.
- To investigate correlations between mRNA half-lives and other molecular features.
- To explore the relationship between mRNA turnover and protein complex stoichiometry.
Main Methods:
- Utilized DNA microarrays for high-throughput mRNA decay measurement.
- Employed a temperature-sensitive RNA polymerase II mutant in yeast.
- Inactivated RNA polymerase II to initiate synchronized mRNA decay analysis.
Main Results:
- Yeast mRNA half-lives exhibit wide variation (3 min to >90 min).
- No straightforward correlation was found between mRNA half-life and ORF size, codon bias, ribosome density, or abundance.
- Decay rates of mRNAs encoding proteins in stoichiometric complexes were generally well-matched.
Conclusions:
- Precise control over individual mRNA decay is a fundamental aspect of yeast gene expression.
- mRNA turnover rates appear linked to protein complex formation and physiological function.
- These findings highlight the sophisticated regulatory mechanisms governing mRNA stability in eukaryotes.