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Dynamic analysis of stochastic transcription cycles

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Harper, Claire V., Finkenstädt, Bärbel, Woodcock, Dan J., Friedrichsen, Sönke, Semprini, Sabrina, Ashall, Louise, Spiller, David G., Mullins, John J., Rand, D. A. (David A.), Davis, Julian R. E. and White, Michael R. H.. (2011) Dynamic analysis of stochastic transcription cycles. PLos Biology, Vol.9 (No.4). ISSN 1545-7885

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Official URL: http://dx.doi.org/10.1371/journal.pbio.1000607

Abstract

In individual mammalian cells the expression of some genes such as prolactin is highly variable over time and has been suggested to occur in stochastic pulses. To investigate the origins of this behavior and to understand its functional relevance, we quantitatively analyzed this variability using new mathematical tools that allowed us to reconstruct dynamic transcription rates of different reporter genes controlled by identical promoters in the same living cell. Quantitative microscopic analysis of two reporter genes, firefly luciferase and destabilized EGFP, was used to analyze the dynamics of prolactin promoter-directed gene expression in living individual clonal and primary pituitary cells over periods of up to 25 h. We quantified the time-dependence and cyclicity of the transcription pulses and estimated the length and variation of active and inactive transcription phases. We showed an average cycle period of approximately 11 h and demonstrated that while the measured time distribution of active phases agreed with commonly accepted models of transcription, the inactive phases were differently distributed and showed strong memory, with a refractory period of transcriptional inactivation close to 3 h. Cycles in transcription occurred at two distinct prolactin-promoter controlled reporter genes in the same individual clonal or primary cells. However, the timing of the cycles was independent and out-of-phase. For the first time, we have analyzed transcription dynamics from two equivalent loci in real-time in single cells. In unstimulated conditions, cells showed independent transcription dynamics at each locus. A key result from these analyses was the evidence for a minimum refractory period in the inactive-phase of transcription. The response to acute signals and the result of manipulation of histone acetylation was consistent with the hypothesis that this refractory period corresponded to a phase of chromatin remodeling which significantly increased the cyclicity. Stochastically timed bursts of transcription in an apparently random subset of cells in a tissue may thus produce an overall coordinated but heterogeneous phenotype capable of acute responses to stimuli.

Item Type:	Journal Article
Subjects:	Q Science > QA Mathematics Q Science > QH Natural history > QH426 Genetics
Divisions:	Faculty of Science > Statistics Faculty of Science > Centre for Systems Biology
Library of Congress Subject Headings (LCSH):	Gene expression -- Mathematical models, Prolactin -- Mathematical models, Genetic transcription -- Mathematical models
Journal or Publication Title:	PLos Biology
Publisher:	Public Library of Science
ISSN:	1545-7885
Date:	12 April 2011
Volume:	Vol.9
Number:	No.4
Identification Number:	10.1371/journal.pbio.1000607
Status:	Peer Reviewed
Access rights to Published version:	Open Access
Funder:	Engineering and Physical Sciences Research Council (EPSRC), Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Wellcome Trust (London, England), European Union (EU), British Heart Foundation, Manchester Academic Health Sciences Centre (MAHSC), National Institute for Health Research (Great Britain) (NIHR)
Grant number:	67252 (WT), GR/S29256/01 (EPSRC), GR/S29256/01 (EPSRC), BB/F005938/1 (BBSRC), 005137 (EU), BBE0129651 (BBSRC)
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URI:	http://wrap.warwick.ac.uk/id/eprint/34842