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Updated: Aug 1, 2025

Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains

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Published on: December 13, 2014

Condition-specific 3' mRNA isoform half-lives and stability elements in yeast.

Joseph V Geisberg¹, Zarmik Moqtaderi¹, Kevin Struhl¹

¹Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.

Proceedings of the National Academy of Sciences of the United States of America

|April 24, 2023

Summary

Environmental conditions impact messenger RNA (mRNA) isoform stability and structure in yeast. While stability generally increases with slower growth, specific regulatory elements appear condition-dependent, suggesting a role in adaptation.

Keywords:

mRNA 3′ end formation mRNA stability elements polyadenylation regulated mRNA turnover yeast

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Area of Science:

Molecular Biology
Genetics
Biochemistry

Background:

Alternative polyadenylation generates diverse 3' mRNA isoforms with varying stability, structure, and function.
These isoforms offer a tool to map regulatory elements within 3' untranslated regions (3'UTRs).

Purpose of the Study:

To investigate the impact of environmental conditions on 3' mRNA isoform turnover and structure in yeast.
To identify condition-specific mRNA stability elements and their functional implications.

Main Methods:

Transcriptome-wide analysis of mRNA isoform stability and structure.
Dimethyl sulfate probing to assess RNA structure.
Correlation analysis of isoform half-lives across different growth conditions.

Main Results:

mRNA isoform stability generally increases under slower growth conditions.
Individual 3' isoforms exhibit conserved structures across conditions, unlike variations within a single condition.
Most mRNA stability elements function in a condition-specific manner.
Condition-specific stability elements are linked to distinct gene functional categories.
No corresponding condition-specific changes in steady-state mRNA isoform levels were observed.

Conclusions:

Regulated mRNA stability may contribute to yeast adaptation to diverse growth environments.
A compensatory relationship between polyadenylation and stability is suggested.
Condition-specific mRNA stability elements likely reflect condition-specific regulation of mRNA 3' end formation.