Chromatin decouples promoter threshold from dynamic range

Abstract

Chromatin influences gene expression by restricting access of DNA binding proteins to their cognate sites in the genome1,2,3. Large-scale characterization of nucleosome positioning in Saccharomyces cerevisiae has revealed a stereotyped promoter organization in which a nucleosome-free region (NFR) is present within several hundred base pairs upstream of the translation start site4,5. Many transcription factors bind within NFRs and nucleate chromatin remodelling events which then expose other cis-regulatory elements6,7,8,9. However, it is not clear how transcription-factor binding and chromatin influence quantitative attributes of gene expression. Here we show that nucleosomes function largely to decouple the threshold of induction from dynamic range. With a series of variants of one promoter, we establish that the affinity of exposed binding sites is a primary determinant of the level of physiological stimulus necessary for substantial gene activation, and sites located within nucleosomal regions serve to scale expression once chromatin is remodelled. Furthermore, we find that the S. cerevisiae phosphate response (PHO) pathway exploits these promoter designs to tailor gene expression to different environmental phosphate levels. Our results suggest that the interplay of chromatin and binding-site affinity provides a mechanism for fine-tuning responses to the same cellular state. Moreover, these findings may be a starting point for more detailed models of eukaryotic transcriptional control.

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Figure 1: PHO5 promoter variants and quantitative expression behaviour.
Figure 2: Promoter architecture and quantitative expression behaviour of representative PHO genes.
Figure 3: Maximum expression of PHO5 promoter variants.
Figure 4: Pho4 binding in vivo to PHO promoters, and model of threshold-dynamic range decoupling.

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Acknowledgements

We thank: S. J. Maerkl and S. R. Quake for sharing Pho4-binding data; J. S. Weissman, H. Li, R. Losick, B. Stern and present and former members of the O’Shea laboratory for discussion and commentary on the manuscript; B. S. Margolin for strain EY1995 and assistance with cell sorting; and B. E. Shakhnovich for assistance with motif analysis. Support was provided by the National Institutes of Health, the Howard Hughes Medical Institute, the David and Lucile Packard Foundation (E.K.O.), and the Burroughs Wellcome Fund (F.H.L.).

Author Contributions F.H.L., D.J.S. and E.K.O. designed the experiments. D.J.S. made initial promoter variants and preliminary measurements of expression behaviour and nucleosome positions. F.H.L. conducted further strain construction, kinetic and steady-state expression measurements, flow cytometry, nucleosome mapping, chromatin immunoprecipitation and computational analysis. F.H.L. and E.K.O. wrote the manuscript.

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Correspondence to Erin K. O’Shea.

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Supplementary information

The file contains Supplementary Methods; Supplementary Discussion; Supplementary Figures 1-10 and Legends; Supplementary Tables 1-7. (PDF 2287 kb)

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Lam, F., Steger, D. & O’Shea, E. Chromatin decouples promoter threshold from dynamic range. Nature 453, 246–250 (2008) doi:10.1038/nature06867

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