Single cell visualization of transcription kinetics variance of highly mobile identical genes using 3D nanoimaging
Open accessAbstract
Multi-cell biochemical assays and single cell fluorescence measurements revealed that the elongation rate of Polymerase II (PolII) in eukaryotes varies largely across different cell types and genes. However, there is not yet a consensus whether intrinsic factors such as the position, local mobility or the engagement by an active molecular mechanism of a genetic locus could be the determinants of the observed heterogeneity. Here by employing high-speed 3D fluorescence nanoimaging techniques we resolve and track at the single cell level multiple, distinct regions of mRNA synthesis within the model system of a large transgene array. We demonstrate that these regions are active transcription sites that release mRNA molecules in the nucleoplasm. Using fluctuation spectroscopy and the phasor analysis approach we were able to extract the local PolII elongation rate at each site as a function of time. We measured a four-fold variation in the average elongation between identical copies of the same gene measured simultaneously within the same cell, demonstrating a correlation between local transcription kinetics and the movement of the transcription site. Together these observations demonstrate that local factors, such as chromatin local mobility and the microenvironment of the transcription site, are an important source of transcription kinetics variability.
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A fourfold variation in RNA Pol II velocity was measured between identical copies of the same gene.
“Indeed, in this latter study, a fourfold variation in RNA Pol II velocity was measured between identical copies of the same gene and overall, the different RNA Pol II speeds measured in the gene array almost span the range of transcription speeds reported using the MS2 containing constructs, from below 0.6 kb/min to over 12 kb/min (Annibale & Gratton, 2015).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Annibale & Gratton, 2015
Other imaging techniques reported RNA Pol II speed between 0.6 and 12 kb/min.
“Other imaging techniques such as fluctuation analysis of fluorescently labeled nascent RNA or high‐speed 3D fluorescence nanoimaging techniques reported speed in the same range, albeit slightly higher between 0.6 and 12 kb/min (Larson et al, 2011; Martin et al, 2013; Annibale & Gratton, 2015).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Annibale & Gratton, 2015
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- Authors
- Annibale, P., & Gratton, E.
- Affiliations
- University of California, Irvine (US)
- Corresponding author
- Gratton, Enrico
- Venue
- Scientific Reports
- Published
- 2015-03-19
- Volume
- 5
- Issue
- 1
- Pages
- 9258-9258
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC4365385
- OpenAlex
- W2036152181
- Cited by
- 24
- References
- 49
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 3 · 2022: 2 · 2021: 3 · 2020: 1 · 2019: 3 · 2018: 4 · 2017: 2 · 2016: 1 · 2015: 1
- FWCI
- 1.16
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Reports (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- arXiv (Cornell University)
- Funders
- National Institutes of Health (GM-076516, GM103540)
- National Institute of General Medical Sciences (P41GM103540, P50GM076516)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- transcription kinetics, transcriptional heterogeneity, single-cell fluorescence imaging, fluctuation spectroscopy, phasor analysis, chromatin mobility, mRNA synthesis, gene expression variation
- MeSH terms
- Cell Nucleus, Chromatin, Humans, Kinetics, Models, Genetic, RNA Polymerase II, RNA, Messenger, Transcription, Genetic, Microscopy, Confocal, Nanotechnology, Cell Line, Tumor, Single-Cell Analysis
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