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TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation


Transcription of eukaryotic messenger RNA (mRNA) encoding genes by RNA polymerase II (Pol II) is triggered by the binding of transactivating proteins to enhancer DNA, which stimulates the recruitment of general transcription factors (TFIIA, B, D, E, F, H) and Pol II on the cis-linked promoter, leading to pre-initiation complex formation and transcription1. In TFIID-dependent activation pathways, this general transcription factor containing TATA-box-binding protein is first recruited on the promoter through interaction with activators1,2,3 and cooperates with TFIIA to form a committed pre-initiation complex4. However, neither the mechanisms by which activation signals are communicated between these factors nor the structural organization of the activated pre-initiation complex are known. Here we used cryo-electron microscopy to determine the architecture of nucleoprotein complexes composed of TFIID, TFIIA, the transcriptional activator Rap1 and yeast enhancer–promoter DNA. These structures revealed the mode of binding of Rap1 and TFIIA to TFIID, as well as a reorganization of TFIIA induced by its interaction with Rap1. We propose that this change in position increases the exposure of TATA-box-binding protein within TFIID, consequently enhancing its ability to interact with the promoter. A large Rap1-dependent DNA loop forms between the activator-binding site and the proximal promoter region. This loop is topologically locked by a TFIIA–Rap1 protein bridge that folds over the DNA. These results highlight the role of TFIIA in transcriptional activation, define a molecular mechanism for enhancer–promoter communication and provide structural insights into the pathways of intramolecular communication that convey transcription activation signals through the TFIID complex.

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Figure 1: Location of critical components of the initiation process within various TFIID complexes.
Figure 2: Structure of the initial TFIID–activator–promoter recruitment complex.
Figure 3: Structure of the committed complex.
Figure 4: Model depicting the formation of the activated TFIID complex.

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Data deposits

The electron density maps of the hydrated TFIID, the TFIID–TFIIA–DNA complex and the TFIID–TFIIA–Rap1–DNA complex I and complex II are deposited in the EM Database under accession numbers EM–5175, EM–5178, EM–5176 and EM–5177, respectively.


  1. Burley, S. K. & Roeder, R. G. Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem. 65, 769–799 (1996)

    Article  CAS  Google Scholar 

  2. Verrijzer, C. P. & Tjian, R. TAFs mediate transcriptional activation and promoter selectivity. Trends Biochem. Sci. 21, 338–342 (1996)

    Article  CAS  Google Scholar 

  3. Jacq, X. et al. Human TAFII30 is present in a distinct TFIID complex and is required for transcriptional activation by the estrogen receptor. Cell 79, 107–117 (1994)

    Article  CAS  Google Scholar 

  4. Lieberman, P. M. & Berk, A. J. A mechanism for TAFs in transcriptional activation: activation domain enhancement of TFIID-TFIIA–promoter DNA complex formation. Genes Dev. 8, 995–1006 (1994)

    Article  CAS  Google Scholar 

  5. Papai, G. et al. Mapping the initiator binding Taf2 subunit in the structure of hydrated yeast TFIID. Structure 17, 363–373 (2009)

    Article  CAS  Google Scholar 

  6. Elmlund, H. et al. Cryo-EM reveals promoter DNA binding and conformational flexibility of the general transcription factor TFIID. Structure 17, 1442–1452 (2009)

    Article  CAS  Google Scholar 

  7. Grob, P. et al. Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues. Structure 14, 511–520 (2006)

    Article  CAS  Google Scholar 

  8. Leurent, C. et al. Mapping histone fold TAFs within yeast TFIID. EMBO J. 21, 3424–3433 (2002)

    Article  CAS  Google Scholar 

  9. Garbett, K. A., Tripathi, M. K., Cencki, B., Layer, J. H. & Weil, P. A. Yeast TFIID serves as a coactivator for Rap1p by direct protein-protein interaction. Mol. Cell. Biol. 27, 297–311 (2007)

    Article  CAS  Google Scholar 

  10. Sussel, L. & Shore, D. Separation of transcriptional activation and silencing functions of the RAP1-encoded repressor/activator protein 1: isolation of viable mutants affecting both silencing and telomere length. Proc. Natl Acad. Sci. USA 88, 7749–7753 (1991)

    Article  ADS  CAS  Google Scholar 

  11. Lieb, J. D., Liu, X., Botstein, D. & Brown, P. O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association. Nature Genet. 28, 327–334 (2001)

    Article  CAS  Google Scholar 

  12. Liu, W. L. et al. Structures of three distinct activator-TFIID complexes. Genes Dev. 23, 1510–1521 (2009)

    Article  CAS  Google Scholar 

  13. Leurent, C. et al. Mapping key functional sites within yeast TFIID. EMBO J. 23, 719–727 (2004)

    Article  CAS  Google Scholar 

  14. Layer, J. H., Miller, S. G. & Weil, P. A. Direct transactivator-transcription factor IID (TFIID) contacts drive yeast ribosomal protein gene transcription. J. Biol. Chem. 285, 15489–15499 (2010)

    Article  CAS  Google Scholar 

  15. Sanders, S. L., Garbett, K. A. & Weil, P. A. Molecular characterization of Saccharomyces cerevisiae TFIID. Mol. Cell. Biol. 22, 6000–6013 (2002)

    Article  CAS  Google Scholar 

  16. Tan, S., Hunziker, Y., Sargent, D. F. & Richmond, T. J. Crystal structure of a yeast TFIIA/TBP/DNA complex. Nature 381, 127–151 (1996)

    Article  ADS  CAS  Google Scholar 

  17. Geiger, J. H., Hahn, S., Lee, S. & Sigler, P. B. Crystal structure of the yeast TFIIA/TBP/DNA complex. Science 272, 830–836 (1996)

    Article  ADS  CAS  Google Scholar 

  18. Oelgeschlager, T., Chiang, C. M. & Roeder, R. G. Topology and reorganization of a human TFIID–promoter complex. Nature 382, 735–738 (1996)

    Article  ADS  CAS  Google Scholar 

  19. Chalkley, G. E. & Verrijzer, C. P. DNA binding site selection by RNA polymerase II TAFs: a TAF(II)250–TAF(II)150 complex recognizes the initiator. EMBO J. 18, 4835–4845 (1999)

    Article  CAS  Google Scholar 

  20. Mencia, M., Moqtaderi, Z., Geisberg, J. V., Kuras, L. & Struhl, K. Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol. Cell 9, 823–833 (2002)

    Article  CAS  Google Scholar 

  21. Simonetti, A. et al. Structure of the 30S translation initiation complex. Nature 455, 416–420 (2008)

    Article  ADS  CAS  Google Scholar 

  22. Konig, P., Giraldo, R., Chapman, L. & Rhodes, D. The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell 85, 125–136 (1996)

    Article  CAS  Google Scholar 

  23. Morse, R. H. RAP, RAP, open up! New wrinkles for RAP1 in yeast. Trends Genet. 16, 51–53 (2000)

    Article  CAS  Google Scholar 

  24. Bleichenbacher, M., Tan, S. & Richmond, T. J. Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes. J. Mol. Biol. 332, 783–793 (2003)

    Article  CAS  Google Scholar 

  25. Wang, W., Gralla, J. D. & Carey, M. The acidic activator GAL4-AH can stimulate polymerase II transcription by promoting assembly of a closed complex requiring TFIID and TFIIA. Genes Dev. 6, 1716–1727 (1992)

    Article  CAS  Google Scholar 

  26. Lieberman, P. M., Ozer, J. & Gursel, D. B. Requirement for transcription factor IIA (TFIIA)-TFIID recruitment by an activator depends on promoter structure and template competition. Mol. Cell. Biol. 17, 6624–6632 (1997)

    Article  CAS  Google Scholar 

  27. Ozer, J., Bolden, A. H. & Lieberman, P. M. Transcription factor IIA mutations show activator-specific defects and reveal a IIA function distinct from stimulation of TBP-DNA binding. J. Biol. Chem. 271, 11182–11190 (1996)

    Article  CAS  Google Scholar 

  28. Shykind, B. M., Kim, J. & Sharp, P. A. Activation of the TFIID–TFIIA complex with HMG-2. Genes Dev. 9, 1354–1365 (1995)

    Article  CAS  Google Scholar 

  29. Kokubo, T., Swanson, M. J., Nishikawa, J. I., Hinnebusch, A. G. & Nakatani, Y. The yeast TAF145 inhibitory domain and TFIIA competitively bind to TATA-binding protein. Mol. Cell. Biol. 18, 1003–1012 (1998)

    Article  CAS  Google Scholar 

  30. van Heel, M. & Schatz, M. Fourier shell correlation threshold criteria. J. Struct. Biol. 151, 250–262 (2005)

    Article  CAS  Google Scholar 

  31. Sanders, S. L. & Weil, P. A. Identification of two novel TAF subunits of the yeast Saccharomyces cerevisiae TFIID complex. J. Biol. Chem. 275, 13895–13900 (2000)

    Article  CAS  Google Scholar 

  32. Rathjen, J. & Mellor, J. Characterisation of sequences required for RNA initiation from the PGK promoter of Saccharomyces cerevisiae . Nucleic Acids Res. 18, 3219–3225 (1990)

    Article  CAS  Google Scholar 

  33. Ludtke, S. J., Baldwin, P. R. & Chiu, W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97 (1999)

    Article  CAS  Google Scholar 

  34. Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007)

    Article  CAS  Google Scholar 

  35. Heymann, J. B. Bsoft: image and molecular processing in electron microscopy. J. Struct. Biol. 133, 156–169 (2001)

    Article  CAS  Google Scholar 

  36. van Heel, M., Harauz, G., Orlova, E. V., Schmidt, R. & Schatz, M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116, 17–24 (1996)

    Article  CAS  Google Scholar 

  37. Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996)

    Article  CAS  Google Scholar 

  38. Pettersen, E. F. et al. UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)

    Article  CAS  Google Scholar 

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This work was supported by grants from the Institut National de la Santé et de la Recherche Médicale, the Centre National pour la Recherche Scientifique, the Association pour la Recherche sur le Cancer, the Fondation pour la Recherche Médicale, the Agence Nationale pour le Recherche and the European SPINE program (G.P., C.R. and P.S., EU contract number QLG2-CT-00988), and the National Institutes of Health (M.K.T., J.H.L. and P.A.W., National Institutes of Health grant number GM52461).

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Authors and Affiliations



P.S. and P.A.W. initiated the study. M.K.T. purified the complexes and performed the biochemical tests. J.H.L. and M.K.T. participated in the design and production of mutant proteins. C.R. and G.P. performed the looping experiments. P.S. and G.P. prepared the samples for microscopy and recorded the images. G.P. performed the image analysis. The manuscript was prepared and commented on by P.S., P.A.W., M.K.T., J.H.L. and G.P.

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Correspondence to P. Anthony Weil or Patrick Schultz.

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The authors declare no competing financial interests.

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Papai, G., Tripathi, M., Ruhlmann, C. et al. TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation. Nature 465, 956–960 (2010).

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