A quantitative model of transcription factor–activated gene expression

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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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.

Author information

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.

Correspondence to Erin K O'Shea.

Supplementary information

Supplementary Text and Figures

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) doi:10.1038/nsmb.1500

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