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

Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
Cell (Impact Factor: 32.24). 12/2011; 147(7):1484-97. DOI: 10.1016/j.cell.2011.11.051
Source: PubMed


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.

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Available from: Tatjana Trcek,
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    • "Most often, however, such effects are considered in the context of a change in the number of autosomal gene copies that persists throughout an organism's lifetime [13], as, e.g., in the haploinsufficiency of certain genes [14]. It is less often acknowledged that the number of copies of all genes varies over each cell cycle, despite evidence that these variations have measurable consequences [15] [16] [17] [18]. Because of the well-known phenomenon of phase locking of oscillators [19], regular, periodic changes in gene dose are likely to be especially relevant to cellular oscillators that depend on gene expression. "
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    • "It might be useful, then, to search for overrepresented elements in the promoter regions of the genes in the AR/R group. Similarly to the experiments in Trcek et al. (2011), one could propose an experiment in which a) the promoter region of some of the AR/R genes is replaced, to test whether the mRNA still retains rhythmicity (i.e., full posttranscriptional clock control), or b) one of these promoter regions is placed upstream of a reporter gene, to see if this gene now displays the rhythmic expression profile of the endogenous one (coupling). With such mechanism in mind, one could argue, however, that the only thing required for the rhythmic profile displayed by these genes in the AR/R group is a protein or ncRNA to bind to the mRNA and somehow mediate its rhythmicity: there would be no need to require this to happen cotranscriptionally or even in the nucleus. "
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    • "Additionally, a considerable fraction of transcript molecules per gene display differing stabilities (Supplementary Fig S3B and C). Although differences in the 5′ UTR may also contribute to RNA decay (Trcek et al, 2011), our results demonstrate genome‐wide that multiple mRNA messages encoding the same protein‐coding sequence that differ only in their 3′ UTR can have divergent post‐transcriptional lifetimes. This finding is in agreement with previous reports describing the potential role of the 3′ UTR in regulating stability and represents the first such genome‐wide confirmation in yeast (Goodarzi et al, 2012; Allen et al, 2013; Ray et al, 2013). "
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