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Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis

Nature Structural & Molecular Biology volume 19, pages 797–802 (2012)Cite this article

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Abstract

Gene expression is inherently stochastic; precise gene regulation by transcription factors is important for cell-fate determination. Many transcription factors regulate their own expression, suggesting that autoregulation counters intrinsic stochasticity in gene expression. Using a new strategy, cotranslational activation by cleavage (CoTrAC), we probed the stochastic expression dynamics of cI, which encodes the bacteriophage λ repressor CI, a fate-determining transcription factor. CI concentration fluctuations influence both lysogenic stability and induction of bacteriophage λ. We found that the intrinsic stochasticity in cI expression was largely determined by CI expression level irrespective of autoregulation. Furthermore, extrinsic, cell-to-cell variation was primarily responsible for CI concentration fluctuations, and negative autoregulation minimized CI concentration heterogeneity by counteracting extrinsic noise and introducing memory. This quantitative study of transcription factor expression dynamics sheds light on the mechanisms cells use to control noise in gene regulatory networks.

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Figure 1: Overview and validation of the CoTrAC strategy.
Figure 2: CoTrAC analysis of stochastic expression of CI in different regulatory contexts.
Figure 3: Time-dependent noise analysis of CI expression.
Figure 4: Dependence of intrinsic noise, extrinsic noise and memory on genetic regulatory context.

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  • 15 July 2012

    In the version of this article initially published online, equations 1 and 3 contained errors. These have been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

We thank J. Little (University of Arizona), D. Finley (Harvard Medical School), R. Baker (John Curtin School of Medical Research) and the Yale University Coli Genetic Stock Center for strains and reagents. Funding provided by National Science Foundation CAREER Award 0746796 (to J.X.), March of Dimes Research grant 1-FY2011 (to J.X.), March of Dimes Basil O'Connor Starter Scholar Research Award 5-FY20 (to J.X.) and National Science Foundation Emerging Frontiers Award 0926287 (to J.W.).

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Author notes

  1. Zach Hensel and Haidong Feng: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Zach Hensel, Christine Hatem & Jie Xiao

  2. Department of Chemistry and Physics, Stony Brook University, Stony Brook, New York, USA

    Haidong Feng, Bo Han & Jin Wang

  3. State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, China

    Jin Wang

  4. College of Physics and State Key Laboratory of Superhard Materials, Jilin University, Changchun, China

    Jin Wang

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Contributions

Z.H. and J.X. designed experiments. Z.H. and C.H. engineered strains and performed immunoblotting experiments. Z.H. acquired and analyzed fluorescence images. H.F., Z.H., B.H., J.X. and J.W. developed analytical methods. Z.H., H.F. and J.X. analyzed data. Z.H., J.X., H.F. and J.W. wrote the manuscript.

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Correspondence to Jin Wang or Jie Xiao.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figs 1–4, Supplementary Tables 1–5 and Supplementary Notes 1 and 2 (PDF 3229 kb)

Supplementary Movie 1

Timelapse fluorescence images for strain λWT (MOV 1422 kb)

Supplementary Movie 2

Timelapse fluorescence images for strain λr3 (MOV 2032 kb)

Supplementary Movie 3

Timelapse fluorescence images for strain λb (MOV 1457 kb)

Supplementary Movie 4

Timelapse fluorescence images for strain λ– (MOV 1083 kb)

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Hensel, Z., Feng, H., Han, B. et al. Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis. Nat Struct Mol Biol 19, 797–802 (2012). https://doi.org/10.1038/nsmb.2336

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