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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.


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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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