Bursts and pulses: Insights from single cell studies into transcriptional mechanisms
Abstract
With a developing appreciation of how noisy gene expression can be, and difficulties in deciphering conventional gene expression data into cell control mechanisms, it has become clear that single cell techniques for measuring transcription are necessary to illuminate basic cell regulation strategies. The resultant use of in situ hybridisation and live cell RNA visualisation approaches in single cells revealed transcription is not adequately reflected by the smooth, seamless process we tend to infer from standard measures of RNA level. When RNA production is measured in single cells, the process of transcription has been shown to occur in bursts, or pulses. This review will highlight the evidence for these phenomena, the proposed mechanisms underlying discontinuity, and the biological implications of such behaviour.
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In eukaryotic cells, transcription occurs in cycles.
“In eukaryotic cells, transcription occurs in cycles [50,51,52].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [50]
Cites
Stochastic Gene Expression in a Single Cell
Elowitz, M. B., Levine, A. J., Siggia, E. D., & Swain, P. S. (2002) · Science · doi:10.1126/science.1070919 · Cited by 5,441 · see citing works
Bacterial Persistence as a Phenotypic Switch
Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L., & Leibler, S. (2004) · Science · doi:10.1126/science.1099390 · Cited by 2,952 · see citing works
Imaging individual mRNA molecules using multiple singly labeled probes
Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A., & Tyagi, S. (2008) · Nature Methods · doi:10.1038/nmeth.1253 · Cited by 2,028 · see citing works
Stochastic mRNA Synthesis in Mammalian Cells
Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y., & Tyagi, S. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040309 · Cited by 1,737 · see citing works
Control of Stochasticity in Eukaryotic Gene Expression
Raser, J. M., & O'Shea, E. K. (2004) · Science · doi:10.1126/science.1098641 · Cited by 1,425 · see citing works
Noise in protein expression scales with natural protein abundance
Bar-Even, A., Paulsson, J., Maheshri, N., Carmi, M., O'Shea, E., Pilpel, Y., & Barkai, N. (2006) · Nature Genetics · doi:10.1038/ng1807 · Cited by 807 · see citing works
Single-RNA counting reveals alternative modes of gene expression in yeast
Zenklusen, D., Larson, D. R., & Singer, R. H. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1514 · Cited by 684 · see citing works
Defining mechanisms that regulate RNA polymerase II transcription in vivo
Fuda, N. J., Ardehali, M. B., & Lis, J. T. (2009) · Nature · doi:10.1038/nature08449 · Cited by 576 · see citing works
Ultradian hormone stimulation induces glucocorticoid receptor-mediated pulses of gene transcription
Stavreva, D. A., Wiench, M., John, S., Conway-Campbell, B. L., McKenna, M. A., Pooley, J. R., Johnson, T. A., Voss, T. C., Lightman, S. L., & Hager, G. L. (2009) · Nature Cell Biology · doi:10.1038/ncb1922 · Cited by 375 · see citing works
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Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity
Martin, R. M., Rino, J., Carvalho, C., Kirchhausen, T., & Carmo-Fonseca, M. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.08.013 · Cited by 173 · see citing works
Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cells
Domingues, A. F., Kulkarni, R., Giotopoulos, G., Gupta, S., Vinnenberg, L., Arede, L., Foerner, E., Khalili, M., Adao, R. R., Johns, A., et al. (2020) · eLife · doi:10.7554/elife.51754 · Cited by 52 · see citing works
Enhancer Function in the 3D Genome
Razin, S. V., Ulianov, S. V., & Iarovaia, O. V. (2023) · Genes · doi:10.3390/genes14061277 · Cited by 15 · see citing works
- Authors
- Chubb, J. R., & Liverpool, T. B.
- Affiliations
- University of Dundee (GB)
- University of Bristol (GB)
- Corresponding author
- Chubb, Jonathan R
- Liverpool, Tanniemola B
- Venue
- Current Opinion in Genetics & Development
- Publisher
- Elsevier BV
- Published
- 2010-10
- Volume
- 20
- Issue
- 5
- Pages
- 478-484
- ISSN
- 0959-437X (ISSN-L)
- OpenAlex
- W2117915703
- Cited by
- 91
- References
- 9
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 4 · 2023: 3 · 2022: 4 · 2021: 4 · 2020: 7 · 2019: 3 · 2018: 5 · 2017: 5 · 2016: 5 · 2015: 7 · 2014: 5 · 2013: 16 · 2012: 7
- FWCI
- 0.93
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Current Opinion in Genetics & Development (publishedVersion)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (publishedVersion)
- Bristol Research (University of Bristol) (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- 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 › Single-cell and spatial transcriptomics
- Keywords
- transcriptional bursting, stochastic gene expression, in situ hybridization, cell-to-cell variability, transcriptional regulation
- MeSH terms
- RNA, Transcription, Genetic, Gene Expression, In Situ Hybridization, Fluorescence, Single-Cell Analysis
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