Analysis of combinatorial cis-regulation in synthetic and genomic promoters

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Abstract

Transcription factor binding sites are being discovered at a rapid pace1,2. It is now necessary to turn attention towards understanding how these sites work in combination to influence gene expression. Quantitative models that accurately predict gene expression from promoter sequence3,4,5 will be a crucial part of solving this problem. Here we present such a model, based on the analysis of synthetic promoter libraries in yeast (Saccharomyces cerevisiae). Thermodynamic models based only on the equilibrium binding of transcription factors to DNA and to each other captured a large fraction of the variation in expression in every library. Thermodynamic analysis of these libraries uncovered several phenomena in our system, including cooperativity and the effects of weak binding sites. When applied to the S. cerevisiae genome, a model of repression by Mig1 (which was trained on synthetic promoters) predicts a number of Mig1-regulated genes that lack significant Mig1-binding sites in their promoters. The success of the thermodynamic approach suggests that the information encoded by combinations of cis-regulatory sites is interpreted primarily through simple protein–DNA and protein–protein interactions, with complicated biochemical reactions—such as nucleosome modifications—being downstream events. Quantitative analyses of synthetic promoter libraries will be an important tool in unravelling the rules underlying combinatorial cis-regulation.

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Figure 1: Gene expression measurements.
Figure 2: Mig1-binding sites act cooperatively, and a weak Mig1 site represses weakly.
Figure 3: Thermodynamic model explains Mig1 repression in the genome.

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Acknowledgements

We thank R. Mitra, G. Stormo, M. Johnston, K. Varley, S. Doniger and members of the Cohen laboratory for discussions and suggestions, and J. Sabina for technical help with LacZ experiments. B.A.C. and J.G. were supported by the NIH (R01 GM078222) and E.D.S. was supported by the NSF (DMR0129848). J.G. was also supported by an NSF Graduate Research Fellowship (DGE-0202737).

Author Contributions J.G. performed all experiments and analyses. B.A.C. and J.G. designed the experiments and wrote the paper. E.D.S. conceived the idea of applying the thermodynamic model to the synthetic promoter libraries, and contributed to its development.

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Correspondence to Barak A. Cohen.

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This file contains Supplementary Methods, Supplementary Figures S1-S4 and Supplementary Tables S1-S9. (PDF 6838 kb)

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Gertz, J., Siggia, E. & Cohen, B. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457, 215–218 (2009) doi:10.1038/nature07521

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