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A quantitative model of transcription factor–activated gene expression

Nature Structural & Molecular Biology volume 15, pages 1192–1198 (2008)Cite this article

Abstract

A challenge facing biology is to develop quantitative, predictive models of gene regulation. Eukaryotic promoters contain transcription factor binding sites of differing affinity and accessibility, but we understand little about how these variables combine to generate a fine-tuned, quantitative transcriptional response. Here we used the PHO5 promoter in budding yeast to quantify the relationship between transcription factor input and gene expression output, termed the gene-regulation function (GRF). A model that captures variable interactions between transcription factors, nucleosomes and the promoter faithfully reproduced the observed quantitative changes in the GRF that occur upon altering the affinity of transcription factor binding sites, and implicates nucleosome-modulated accessibility of transcription factor binding sites in increasing the diversity of gene expression profiles. This work establishes a quantitative framework that can be applied to predict GRFs of other eukaryotic genes.

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Figure 1: Measuring the GRF from the tetracycline-regulated gene expression system.
Figure 2: Raw data of fluorescence intensities from single cells and the fits to GRFs.
Figure 3: The diversity of GRFs and the relationship between the maximum expression level and the nucleosome occupancy over the TATA box region.
Figure 4: Quantitative models of Pho4-dependent chromatin remodeling.
Figure 5: Comparison between the data and the model prediction.

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References

  1. Cyert, M.S. Regulation of nuclear localization during signaling. J. Biol. Chem. 276, 20805–20808 (2001).

    Article  CAS  Google Scholar 

  2. Vogel, K., Horz, W. & Hinnen, A. The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions. Mol. Cell. Biol. 9, 2050–2057 (1989).

    Article  CAS  Google Scholar 

  3. Venter, U., Svaren, J., Schmitz, J., Schmid, A. & Horz, W. A nucleosome precludes binding of the transcription factor Pho4 in vivo to a critical target site in the PHO5 promoter. EMBO J. 13, 4848–4855 (1994).

    Article  CAS  Google Scholar 

  4. Lam, F.H., Steger, D.J. & O'Shea, E.K. Chromatin decouples promoter threshold from dynamic range. Nature 453, 246–250 (2008).

    Article  CAS  Google Scholar 

  5. Barbaric, S., Reinke, H. & Horz, W. Multiple mechanistically distinct functions of SAGA at the PHO5 promoter. Mol. Cell. Biol. 23, 3468–3476 (2003).

    Article  CAS  Google Scholar 

  6. Steger, D.J., Haswell, E.S., Miller, A.L., Wente, S.R. & O'Shea, E.K. Regulation of chromatin remodeling by inositol polyphosphates. Science 299, 114–116 (2003).

    Article  CAS  Google Scholar 

  7. Dhasarathy, A. & Kladde, M.P. Promoter occupancy is a major determinant of chromatin remodeling enzyme requirements. Mol. Cell. Biol. 25, 2698–2707 (2005).

    Article  CAS  Google Scholar 

  8. Reinke, H. & Horz, W. Histories are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 11, 1599–1607 (2003).

    Article  CAS  Google Scholar 

  9. Boeger, H., Griesenbeck, J., Strattan, J.S. & Kornberg, R.D. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11, 1587–1598 (2003).

    Article  CAS  Google Scholar 

  10. Adkins, M.W., Howar, S.R. & Tyler, J.K. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol. Cell 14, 657–666 (2004).

    Article  CAS  Google Scholar 

  11. Adkins, M.W., Williams, S.K., Linger, J. & Tyler, J.K. Chromatin disassembly from the PHO5 promoter is essential for the recruitment of the general transcription machinery and coactivators. Mol. Cell. Biol. 27, 6372–6382 (2007).

    Article  CAS  Google Scholar 

  12. Adkins, M.W. & Tyler, J.K. Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions. Mol. Cell 21, 405–416 (2006).

    Article  CAS  Google Scholar 

  13. Bintu, L. et al. Transcriptional regulation by the numbers: applications. Curr. Opin. Genet. Dev. 15, 125–135 (2005).

    Article  CAS  Google Scholar 

  14. Rosenfeld, N., Young, J.W., Alon, U., Swain, P.S. & Elowitz, M.B. Gene regulation at the single-cell level. Science 307, 1962–1965 (2005).

    Article  CAS  Google Scholar 

  15. Kalisky, T., Dekel, E. & Alon, U. Cost-benefit theory and optimal design of gene regulation functions. Phys. Biol. 4, 229–245 (2007).

    Article  CAS  Google Scholar 

  16. Komeili, A. & O'Shea, E.K. Roles of phosphorylation sites in regulating activity of the transcription factor Pho4. Science 284, 977–980 (1999).

    Article  CAS  Google Scholar 

  17. Springer, M., Wykoff, D.D., Miller, N. & O'Shea, E.K. Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes. PLoS Biol. 1, e8 (2003).

    Article  Google Scholar 

  18. Becskei, A., Kaufmann, B.B. & van Oudenaarden, A. Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat. Genet. 37, 937–944 (2005).

    Article  CAS  Google Scholar 

  19. Sheff, M.A. & Thorn, K.S. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 21, 661–670 (2004).

    Article  CAS  Google Scholar 

  20. Rizzo, M.A., Springer, G.H., Granada, B. & Piston, D.W. An improved cyan fluorescent protein variant useful for FRET. Nat. Biotechnol. 22, 445–449 (2004).

    Article  CAS  Google Scholar 

  21. Shimizu, T. et al. Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition. EMBO J. 16, 4689–4697 (1997).

    Article  CAS  Google Scholar 

  22. Raser, J.M. & O'Shea, E.K. Control of stochasticity in eukaryotic gene expression. Science 304, 1811–1814 (2004).

    Article  CAS  Google Scholar 

  23. Zhang, H. & Reese, J.C. Exposing the core promoter is sufficient to activate transcription and alter coactivator requirement at RNR3. Proc. Natl. Acad. Sci. USA 104, 8833–8838 (2007).

    Article  CAS  Google Scholar 

  24. Barbaric, S., Munsterkotter, M., Goding, C. & Horz, W. Cooperative Pho2-Pho4 interactions at the PHO5 promoter are critical for binding of Pho4 to UASp1 and for efficient transactivation by Pho4 at UASp2. Mol. Cell. Biol. 18, 2629–2639 (1998).

    Article  CAS  Google Scholar 

  25. Nourani, A., Utley, R.T., Allard, S. & Cote, J. Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation. EMBO J. 23, 2597–2607 (2004).

    Article  CAS  Google Scholar 

  26. Jessen, W.J., Hoose, S.A., Kilgore, J.A. & Kladde, M.P. Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters. Nat. Struct. Mol. Biol. 13, 256–263 (2006).

    Article  CAS  Google Scholar 

  27. Maerkl, S.J. & Quake, S.R. A systems approach to measuring the binding energy landscapes of transcription factors. Science 315, 233–237 (2007).

    Article  CAS  Google Scholar 

  28. Gregory, P.D., Barbaric, S. & Horz, W. Analyzing chromatin structure and transcription factor binding in yeast. Methods 15, 295–302 (1998).

    Article  CAS  Google Scholar 

  29. Schmid, A., Fascher, K.D. & Horz, W. Nucleosome disruption at the yeast PHO5 promoter upon PHO5 induction occurs in the absence of DNA replication. Cell 71, 853–864 (1992).

    Article  CAS  Google Scholar 

  30. Nalley, K., Johnston, S.A. & Kodadek, T. Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo. Nature 442, 1054–1057 (2006).

    Article  CAS  Google Scholar 

  31. Yao, J., Munson, K.M., Webb, W.W. & Lis, J.T. Dynamics of heat shock factor association with native gene loci in living cells. Nature 442, 1050–1053 (2006).

    Article  CAS  Google Scholar 

  32. Karpova, T.S. et al. Concurrent fast and slow cycling of a transcriptional activator at an endogenous promoter. Science 319, 466–469 (2008).

    Article  CAS  Google Scholar 

  33. Segal, E., Raveh-Sadka, T., Schroeder, M., Unnerstall, U. & Gaul, U. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451, 535–540 (2008).

    Article  CAS  Google Scholar 

  34. Boeger, H., Griesenbeck, J. & Kornberg, R.D. Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell 133, 716–726 (2008).

    Article  CAS  Google Scholar 

  35. Cairns, B.R. Chromatin remodeling: insights and intrigue from single-molecule studies. Nat. Struct. Mol. Biol. 14, 989–996 (2007).

    Article  CAS  Google Scholar 

  36. Urlinger, S. et al. Exploring the sequence space for tetracycline-dependent transcriptional activators: novel mutations yield expanded range and sensitivity. Proc. Natl. Acad. Sci. USA 97, 7963–7968 (2000).

    Article  CAS  Google Scholar 

  37. Gari, E., Piedrafita, L., Aldea, M. & Herrero, E. A set of vectors with a tetracycline-regulatable promoter system for modulated gene expression in Saccharomyces cerevisiae. Yeast 13, 837–848 (1997).

    Article  CAS  Google Scholar 

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Acknowledgements

We are especially grateful to F. Lam, Whitehead Institute, Cambridge, for the series of PHO5 promoter variant strains and protocols for ChIP and qPCR, and B. Margolin, University of California at San Francisco, for assistance with basic yeast techniques and helpful discussions. We thank members of the O'Shea laboratory, the Xie laboratory and the Bauer center as well as anonymous reviewers for advice and comments on the manuscript. We also thank A. van Oudenaarden, Massachusetts Institute of Technology, Cambridge, for the gift of the TETO7 plasmid. H.D.K. is supported by a CASI award from the Burroughs Wellcome Fund. E.K.O. acknowledges support from the US National Institutes of Health grant GM51377 and the Howard Hughes Medical Institute.

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Authors and Affiliations

  1. Departments of Molecular and Cellular Biology, Howard Hughes Medical Institute, and Chemistry and Chemical Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Northwest Laboratories, 52 Oxford Street, Room 445.40, Cambridge, 02138, Massachusetts, USA

    Harold D Kim & Erin K O'Shea

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  1. Harold D Kim
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Contributions

H.D.K. and E.K.O. designed the research; H.D.K. performed the experiments; H.D.K. analyzed the data; H.D.K. and E.K.O. wrote the paper.

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Correspondence to Erin K O'Shea.

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Supplementary Figures 1–6, Supplementary Methods and Supplementary Discussion (PDF 260 kb)

Supplementary Data

Fluorescence Data (XLS 4283 kb)

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Kim, H., O'Shea, E. A quantitative model of transcription factor–activated gene expression. Nat Struct Mol Biol 15, 1192–1198 (2008). https://doi.org/10.1038/nsmb.1500

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