Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast

• Published in: Cell 2011-12, Vol.147 (7), p.1484-1497
• Main Authors: Trcek, Tatjana, Larson, Daniel R., Moldón, Alberto, Query, Charles C., Singer, Robert H.
• Format: Article
• Language: English
• Subjects: Cell Cycle; Cell Cycle Proteins - genetics; Cell Cycle Proteins - metabolism; Cyclin B - genetics; Gene Expression Regulation, Fungal; In Situ Hybridization, Fluorescence; Kinetics; Promoter Regions, Genetic; Protein-Serine-Threonine Kinases - metabolism; RNA Stability; Saccharomyces cerevisiae - cytology; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Transcription Factors - genetics; Transcription, Genetic
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2011.11.051

Messenger RNA decay measurements are typically performed on a population of cells. However, this approach cannot reveal sufficient complexity to provide information on mechanisms that may regulate mRNA degradation, possibly on short timescales. To address this deficiency, we measured cell cycle-regulated decay in single yeast cells using single-molecule FISH. We found that two genes responsible for mitotic progression, SWI5 and CLB2, exhibit a mitosis-dependent mRNA stability switch. Their transcripts are stable until mitosis, when a precipitous decay eliminates the mRNA complement, preventing carryover into the next cycle. Remarkably, the specificity and timing of decay is entirely regulated by their promoter, independent of specific cis mRNA sequences. The mitotic exit network protein Dbf2p binds to SWI5 and CLB2 mRNAs cotranscriptionally and regulates their decay. This work reveals the promoter-dependent control of mRNA stability, a regulatory mechanism that could be employed by a variety of mRNAs and organisms. [Display omitted] ► mRNA turnover was quantified in unperturbed yeast cells using single-molecule FISH ► SWI5 and CLB2 exhibit a mitosis-dependent switch in their mRNA stability ► Their decay is promoter regulated and independent of cis mRNA sequences ► Dbf2p binds to SWI5 and CLB2 cotranscriptionally and regulates their stability Control of promoter-mediated mRNA decay extends beyond transcription factors to include kinases previously associated with the cell cycle.