Abstract
Recent advances in measuring gene expression at the single-cell level have highlighted the stochastic nature of messenger RNA and protein synthesis1,2,3. Stochastic gene expression creates a source of variability in the abundance of cellular components, even among isogenic cells exposed to an identical environment. Recent integrated experimental and modelling studies4,5,6,7,8,9,10,11,12,13 have shed light on the molecular sources of this variability. However, many of these studies focus on systems that have reached a steady state and therefore do not address a large class of dynamic phenomena including oscillatory gene expression. Here we develop a general protocol for analysing and predicting stochastic gene expression in systems that never reach steady states. We use this framework to analyse experimentally stochastic expression of genes driven by the Synechococcus elongatus circadian clock. We find that, although the average expression at two points in the circadian cycle separated by 12 hours is identical, the variability at these two time points can be different. We show that this is a general feature of out-of-steady-state systems. We demonstrate how intrinsic noise sources, owing to random births and deaths of mRNAs and proteins, or extrinsic noise sources, which introduce fluctuations in rate constants, affect the cell-to-cell variability. To distinguish experimentally between these sources, we measured how the correlation between expression fluctuations of two identical genes is modulated during the circadian cycle. This quantitative framework is generally applicable to any out-of-steady-state system and will be necessary for understanding the fidelity of dynamic cellular systems.
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Acknowledgements
We thank S. S. Golden and J. L. Ditty for assistance with the initial phase of this work and their gifts of plasmids and strains. We acknowledge I. Lipchin and M. J. T. O’Kelly for assistance with data collection, cloning and bioluminescence measurements. We acknowledge A. Tolonen, S. W. Chisholm, M. Thattai, H. Lim, J. C. Gore and A. Raj for discussions and suggestions. This work was performed in part at the MIT Laser Biomedical Research Center. This work was supported by NSF and NIH grants.
Author Contributions J.R.C. and P.L. performed the experiments. J.M.P. developed the model. J.R.C., .J.M.P. and A.v.O. designed the experiments, interpreted the results and wrote the paper.
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Supplementary Information
This file contains Supplementary experimental and modeling Methods and Materials with Supplementary Figures S1-S2. (PDF 585 kb)
Supplementary Movie 1
This file contains Supplementary Movie 1 demonstrating circadian oscillations in single S. elongatus PCC7942 cells. This file was modified on 31 January 2008 because of the technical difficulties with the file format. (AVI 3601 kb)
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Chabot, J., Pedraza, J., Luitel, P. et al. Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock. Nature 450, 1249–1252 (2007). https://doi.org/10.1038/nature06395
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DOI: https://doi.org/10.1038/nature06395
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