Signal-dependent dynamics of transcription factor translocation controls gene expression

Abstract

Information about environmental stimuli is often transmitted using common signaling molecules, but the mechanisms that ensure signaling specificity are not entirely known. Here we show that the identities and intensities of different stresses are transmitted by modulation of the amplitude, duration or frequency of nuclear translocation of the Saccharomyces cerevisiae general stress response transcription factor Msn2. Through artificial control of the dynamics of Msn2 translocation, we reveal how distinct dynamical schemes differentially affect reporter gene expression. Using a simple model, we predict stress-induced reporter gene expression from single-cell translocation dynamics. We then demonstrate that the response of natural target genes to dynamical modulation of Msn2 translocation is influenced by differences in the kinetics of promoter transitions and transcription factor binding properties. Thus, multiple environmental signals can trigger qualitatively different dynamics of a single transcription factor and influence gene expression patterns.

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Figure 1: Msn2 translocates to the nucleus with different dynamics in response to different stresses.
Figure 2: Quantification of single-cell Msn2-YFP translocation traces.
Figure 3: Experimental and computational analysis of gene expression in response to modulation of Msn2 nuclear translocation dynamics.
Figure 4: The dynamics of Msn2 nuclear translocation influences target gene expression.
Figure 5: The model predicts that target genes have distinct responses to different input regimes.
Figure 6: Analysis of a simplified model.
Figure 7: Microarray analysis to evaluate the model predictions.

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Acknowledgements

We thank S. Ramanathan for help with the microfluidics devices. We thank P. Cluzel, V. Denic, G. Lahav, M. Springer, B. Stern, H. Dohlman, T. Elston and M. Behar for critical comments on the manuscript. We thank X. Zhou in the O'Shea lab for generously providing the unpublished nucleosome profile data, M. Rust and S. Mukherji for insightful suggestions, and other members of the O'Shea lab for helpful discussions. E.K.O. is a Howard Hughes Medical Institute investigator.

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Contributions

N.H. and E.K.O. designed the project. N.H. carried out the experiments and analyzed the data. N.H. and E.K.O. wrote the paper.

Corresponding author

Correspondence to Erin K O'Shea.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–15, Supplementary Results and Supplementary Methods (PDF 6869 kb)

Supplementary Video 1

Time-lapse video of Msn2-YFP in response to 0.1% glucose limitation. (MP4 3256 kb)

Supplementary Video 2

Time-lapse video of Msn2-YFP in response to 0.375 M KCl. (MP4 3297 kb)

Supplementary Video 3

Time-lapse video of Msn2-YFP in response to 0.01 mM H2O2. (MP4 2853 kb)

Supplementary Video 4

Time-lapse video of Msn2-YFP in response to oscillatory 1-NM-PP1 treatment. (MP4 1837 kb)

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Hao, N., O'Shea, E. Signal-dependent dynamics of transcription factor translocation controls gene expression. Nat Struct Mol Biol 19, 31–39 (2012). https://doi.org/10.1038/nsmb.2192

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