Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme

Nature volume 399, pages 609–613 (1999)Cite this article

Abstract

In eukaryotes, transcriptional activators have been proposed to function by recruiting the RNA polymerase II (Pol II) machinery1,2,3, by altering the conformation of this machinery4,5, or by affecting steps after initiation6,7,8, but the evidence is not definitive. Genomic footprinting of yeast TATA-box elements reveals activator-dependent alterations of chromatin structure9 and activator-independent protection10, but little is known about the association of specific components of the Pol II machinery with promoters in vivo. Here we analyse TATA-box-binding-protein (TBP) occupancy of 30 yeast promoters in vivo. We find that TBP association with promoters is stimulated by activators and inhibited by the Cyc8–Tup1 repressor, and that transcriptional activity correlates strongly with the degree of TBP occupancy. In a small subset of promoters, TBP occupancy is higher than expected when gene activity is low, and the activator-dependent increase is modest. TBP association depends on the PolII holoenzyme component Srb4, but not on the Kin28 subunit of the transcription factor TFIIH, even though both proteins aregenerally required for transcription. Thus in yeast cells, TBP association with promoters occurs in concert with the Pol II holoenzyme, activator-dependent recruitment of the Pol II machinery occurs at the vast majority of promoters, and Kin28 acts after the initial recruitment.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: TBP occupancy at GAL and MET promoters.
Figure 2: TBP occupancy in response to heat shock and copper induction.
Figure 3: TBP occupancy at promoters induced during non-fermentative growth.
Figure 4: TBP occupancy at promoters repressed by the Cyc8–Tup1 corepressor complex.
Figure 5: Role of general transcription factors for TBP occupancy at promoters.

Similar content being viewed by others

References

  1. Ptashne, M. & Gann, A. Transcriptional activation by recruitment. Nature 386, 569–577 (1997).

    Article  ADS  CAS  Google Scholar 

  2. Klein, C. & Struhl, K. Increased recruitment of TATA-binding protein to the promoter by transcriptional activation domains in vivo. Science 266, 280–282 (1994).

    Article  ADS  CAS  Google Scholar 

  3. Keaveney, M. & Struhl, K. Activator-mediated recruitment of the RNA polymerase II machinery is the predominant mechanism for transcriptional activation in yeast. Mol. Cell 1, 917–924 (1998).

    Article  CAS  Google Scholar 

  4. Roberts, S. G. & Green, M. R. Activator-induced conformational change in general transcription factor TFIIB. Nature 371, 717–720 (1994).

    Article  ADS  CAS  Google Scholar 

  5. Chi, T. & Carey, M. Assembly of the isomerized TFIIA-TFIID-TATA ternary complex is necessary and sufficient for gene activation. Genes Dev. 10, 2540–2550 (1996).

    Article  CAS  Google Scholar 

  6. Rougvie, A. E. & Lis, J. T. Postinitiation transcriptional control in Drosophila melanogaster. Mol. Cell. Biol. 10, 6041–6045 (1990).

    Article  CAS  Google Scholar 

  7. Yankulov, K., Blau, J., Purton, T., Roberts, S. & Bentley, D. L. Transcriptional elongation by RNA polymerase II is stimulated by transactivators. Cell 77, 749–759 (1994).

    Article  CAS  Google Scholar 

  8. Krumm, A., Hickey, L. B. & Groudine, M. Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. Genes Dev. 9, 559–572 (1995).

    Article  CAS  Google Scholar 

  9. Selleck, S. B. & Majors, J. Photofootprinting in vivo detects transcription-dependent changes in yeast TATA boxes. Nature 325, 173–177 (1987).

    Article  ADS  CAS  Google Scholar 

  10. Chen, J., Ding, M. & Pederson, D. S. Binding of TFIID to the CYC1 TATA boxes in yeast occurs independently of upstream activating sequences. Proc. Natl Acad. Sci. USA 91, 11909–11913 (1994).

    Article  ADS  CAS  Google Scholar 

  11. Strahl-Bolsinger, S., Heckt, A., Luo, K. & Grunstein, M. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11, 83–93 (1997).

    Article  CAS  Google Scholar 

  12. Aparicio, O. M., Weinstein, D. M. & Bell, S. P. Components and dynamics of DNA replication complexes in S. cerevisiae : redistribution of MCM proteins and Cdc45p during S phase. Cell 91, 59–69 (1997).

    Article  CAS  Google Scholar 

  13. Meluh, P. B. & Koshland, D. Budding yeast centromere composition and assembly as revealed by invivo cross-linking. Genes Dev. 11, 3401–3412 (1997).

    Article  CAS  Google Scholar 

  14. Blaiseau, P. L. & Thomas, D. Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. EMBO J. 17, 6327–6336 (1998).

    Article  CAS  Google Scholar 

  15. Keleher, C. A., Redd, M. J., Schultz, J., Carlson, M. & Johnson, A. D. Ssn6-Tup1 is a general repressor of transcription in yeast. Cell 68, 709–719 (1992).

    Article  CAS  Google Scholar 

  16. Tzamarias, D. & Struhl, K. Functional dissection of the yeast Cyc8–Tup1 transcriptional co-repressor complex. Nature 369, 758–761 (1994).

    Article  ADS  CAS  Google Scholar 

  17. Patikoglou, G. & Burley, S. K. Eukaryotic transcription factor–DNA complexes. Annu. Rev. Biophys. Biomol. Struct. 26, 289–325 (1997).

    Article  CAS  Google Scholar 

  18. Thompson, C. M. & Young, R. A. General requirement for RNA polymerase II holoenzymes in vivo. Proc. Natl Acad. Sci. USA 92, 4587–4590 (1995).

    Article  ADS  CAS  Google Scholar 

  19. Nonet, M., Scafe, C., Sexton, J. & Young, R. Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol. Cell. Biol. 7, 1602–1611 (1987).

    Article  CAS  Google Scholar 

  20. Cismowski, M., Laff, G., Soloman, M. & Reed, S. KIN28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol. Cell. Biol. 15, 2983–2992 (1995).

    Article  CAS  Google Scholar 

  21. Hengartner, C. J. et al. Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases. Mol. Cell 2, 43–53 (1998).

    Article  CAS  Google Scholar 

  22. Orphanides, G., Lagrange, T. & Reinberg, D. The general initiation factors of RNA polymerase II. Genes Dev. 10, 2657–2683 (1996).

    Article  CAS  Google Scholar 

  23. Koleske, A. J. & Young, R. A. An RNA polymerase II holoenzyme responsive to activators. Nature 368, 466–469 (1994).

    Article  ADS  CAS  Google Scholar 

  24. Kim, Y.-J., Bjorklund, S., Li, Y., Sayre, M. H. & Kornberg, R. D. Amultiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77, 599–608 (1994).

    Article  CAS  Google Scholar 

  25. Stargell, L. A. & Struhl, K. Anew class of activation-defective TATA-binding protein mutants: Evidence for two steps of transcriptional activation in vivo. Mol. Cell. Biol. 16, 4456–4464 (1996).

    Article  CAS  Google Scholar 

  26. Akhtar, A., Faye, G. & Bentley, D. L. Distinct activated and non-activated RNA polymerase II complexes in yeast. EMBO J. 15, 4654–4664 (1996).

    Article  CAS  Google Scholar 

  27. Gonzalez-Couto, E., Klages, N. & Strubin, M. Synergistic and promoter-selective activation of transcription by recruitment of TFIID and TFIIB. Proc. Natl Acad. Sci. USA 94, 8036–8041 (1997).

    Article  ADS  CAS  Google Scholar 

  28. Cormack, B. P., Strubin, M., Ponticelli, A. S. & Struhl, K. Functional differences between yeast and human TFIID are localized to the highly conserved region. Cell 65, 341–348 (1991).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank M. Benson, J. Geisberg, M. Harrison and S. Reed for DNAs and yeast strains; L. Stargell for TBP antibodies; M. Green for communicating unpublished results; and O. Aparicio, S. Bell and J. Lis for discussion. This work was supported by postdoctoral fellowships to L.K. from the Association pour la Recherche sur le Cancer and the Human Frontier Science Program, and by research grants to K.S. from the NIH.

Author information

Authors and Affiliations

  1. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Laurent Kuras & Kevin Struhl

Authors
  1. Laurent Kuras
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kevin Struhl
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kevin Struhl.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kuras, L., Struhl, K. Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399, 609–613 (1999). https://doi.org/10.1038/21239

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/21239

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing