Cited by 684Gene Regulatory Network AnalysisGenomics and Chromatin DynamicsRNA Research and Splicing

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

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Zenklusen, Daniel, Larson, Daniel R, Singer, Robert H·2008·Nature Structural & Molecular Biology

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Abstract

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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Authors: Zenklusen, D., Larson, D. R., & Singer, R. H.
Affiliations: Albert Einstein College of Medicine (US)
Corresponding author: Singer, Robert H
ORCID: Zenklusen, Daniel
Larson, Daniel R
Singer, Robert H
Venue: Nature Structural & Molecular Biology
Publisher: Springer Science and Business Media LLC
Published: 2008-11-16
Volume: 15
Issue: 12
Pages: 1263-1271
ISSN: 1545-9985 (ISSN-L)
1545-9993
DOI: 10.1038/nsmb.1514
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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Single-RNA counting reveals alternative modes of gene expression in yeast

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