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Single-RNA counting reveals alternative modes of gene expression in yeast
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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.
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“In recent years, single-molecule fluorescence microscopy has been used to count mRNA (12-16) or protein (8, 17) molecules in individual cells, especially in bacteria. However, these methods have only been applied to limited number of specific genes.”
From Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells (2010) · cites this paper as [16]
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“SCM estimates of absolute mRNA levels matched FISH measurements well [53] (average difference of 1.2-fold between estimated and measured levels [Fig 5B], with one outlier estimate overshooting the FISH value by 1.7-fold).”
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Metadata
- Authors
- Zenklusen, D., Larson, D. R., & Singer, R. H.
- Affiliations
- Albert Einstein College of Medicine (US)
- Corresponding author
- Singer, Robert H
- Venue
- Nature Structural & Molecular Biology
- Published
- 2008-11-16
- Volume
- 15
- Issue
- 12
- Pages
- 1263-1271
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC3154325
- OpenAlex
- W1992927069
- Cited by
- 684
- References
- 63
- Citations by year
- 2026: 16 · 2025: 25 · 2024: 45 · 2023: 35 · 2022: 22 · 2021: 38 · 2020: 37 · 2019: 40 · 2018: 44 · 2017: 36 · 2016: 52 · 2015: 47 · 2014: 38 · 2013: 64 · 2012: 40
- FWCI
- 14.41
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM057071)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- transcriptional bursting, gene expression variation, Saccharomyces cerevisiae, PDR5, nascent RNA, mRNA levels, housekeeping genes, transcriptional regulation
- MeSH terms
- RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae, Transcription, Genetic, Trans-Activators, Gene Expression, In Situ Hybridization, Fluorescence, Saccharomyces cerevisiae Proteins
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