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Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome

Nature Structural & Molecular Biology volume 16, pages 1043–1048 (2009)Cite this article

Abstract

Transcription regulation in eukaryotes involves rapid recruitment and proper assembly of transcription factors at gene promoters. To determine the dynamics of the transcription machinery on DNA, we used a differential chromatin immunoprecipitation procedure coupled to whole-genome microarray detection in Saccharomyces cerevisiae. We find that TATA-binding protein (TBP) turnover is low at RNA polymerase I (Pol I) promoters. Whereas RNA polymerase III (Pol III) promoters represent an intermediate case, TBP turnover is high at RNA polymerase II (Pol II) promoters. Within these promoters, the highest turnover correlates with binding of the Spt–Ada–Gcn5 acetyltransferase complex (SAGA) coactivator, Mot1p dependence and presence of a canonical TATA box. In contrast, slow turnover Pol II promoters depend on TFIID and on the gene-specific factor, Rap1p. Together this shows that TBP turnover is regulated by protein factors rather than DNA sequence and argues that TBP turnover is an important determinant in regulating gene expression.

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Figure 1: Induced TBP expression results in TBP exchange at promoters.
Figure 2: TBP turnover at selected promoters.
Figure 3: Genome-wide analysis of TBP turnover.
Figure 4: Analysis of TBP dynamics at the ribosomal DNA (rDNA) locus.
Figure 5: Analysis of a subset of Pol II promoters with distinct TBP turnovers.

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Acknowledgements

We are grateful to M. Groot Koerkamp, D. van Leenen and C. Ko of the University Medical Center (UMC) Utrecht and Utrecht University microarray facility for technical assistance. We are grateful to T. Weil (Vanderbilt University) for providing TBP antibodies. We also thank P. Lijnzaad and H. van Bakel for discussions and G. Spedale, P. Pijnappel and P. de Graaf for critical reading of this manuscript. This work is supported by grants (805.47.080, 825.06.033 and 700.57.302) of the Netherlands Organization for Scientific Research (NWO), the Netherlands Proteomics Centre (NPC) and the EU (Integrated Project EUTRACC, LSHG-CT-2007-037445).

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  1. Folkert J van Werven

    Present address: Present address: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,

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  1. Department of Physiological Chemistry, University Medical Center Utrecht, Utrecht, The Netherlands

    Folkert J van Werven, Hetty A A M van Teeffelen, Frank C P Holstege & H Th Marc Timmers

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Contributions

F.J.v.W. and H.Th.M.T. designed the experiments; F.J.W. and H.A.A.M.v.T. carried out the experiments; F.J.v.W. and H.Th.M.T. analyzed the data; F.C.P.H. provided advice on design of the experiments and data analysis; H.Th.M.T. supervised the experiments and data analysis; F.J.v.W. and H.Th.M.T. wrote the manuscript.

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Correspondence to H Th Marc Timmers.

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van Werven, F., van Teeffelen, H., Holstege, F. et al. Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome. Nat Struct Mol Biol 16, 1043–1048 (2009). https://doi.org/10.1038/nsmb.1674

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