Single-RNA counting reveals alternative modes of gene expression in yeast

By Daniel Zenklusen, D. Larson, R. Singer. Nature Structural &Molecular Biology, 2008

765 citations recorded by the source corpus.

Proper execution of transcriptional programs is a key requirement of gene expression regulation, demanding accurate control of timing and amplitude. How precisely the transcription machinery fulfills this task is not known. Using an in situ hybridization approach that detects single mRNA molecules, we measured mRNA abundance and transcriptional activity within single Saccharomyces cerevisiae cells. We found that expression levels for particular genes are higher than initially reported and can vary substantially among cells. However, variability for most constitutively expressed genes is unexpectedly small. Combining single-transcript measurements with computational modeling indicates that low expression variation is achieved by transcribing genes using single transcription-initiation events that are clearly separated in time, rather than by transcriptional bursts. In contrast, PDR5, a gene regulated by the transcription coactivator complex SAGA, is expressed using transcription bursts, resulting in larger variation. These data directly demonstrate the existence of multiple expression modes used to modulate the transcriptome.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2c073e7e17f1b587dcaaea33fa5e7eed922659cd

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In Molecular Biology

1. A. Senecal
2. Jeetayu Biswas
3. Maria Vera
4. H. Park
5. R. Singer

Citations in the corpus

• Single-Cell and Single-Molecule Analysis of Gene Expression Regulation (2016, methodology): “Analysis of the image obtained by smFISH requires software, such as Localize and Air-Localize (89, 142, 159) or FISH-QUANT (104), to automatically count the number of transcripts in the nucleus and the cytoplasm and to quantify nascent mRNAs at active transcription sites (TSs) in three dimensions.”
• Inaugural Article: Three-dimensional tracking of single mRNA particles in Saccharomyces cerevisiae using a double-helix point spread function (2010, neutral): “Furthermore, ARG3 is expressed at just 1–2 copies per cell (36, 37), thus reducing the potential obfuscation of high-confidence single trajectories by the interference of overlapping signals from distinct particles.”