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. 2010 Jun 17;465(7300):956-60.
doi: 10.1038/nature09080.

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

Gabor Papai  1 , Manish K Tripathi, Christine Ruhlmann, Justin H Layer, P Anthony Weil, Patrick Schultz
Affiliations

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

Gabor Papai et al. Nature. .

Abstract

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 transcription. In TFIID-dependent activation pathways, this general transcription factor containing TATA-box-binding protein is first recruited on the promoter through interaction with activators and cooperates with TFIIA to form a committed pre-initiation complex. 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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Figures

Figure 1
Figure 1. Location of critical components of the initiation process within various TFIID complexes
a, Cryo-EM structure of the yeast holo-TFIID complex. The five major lobes (A, B, C1, C2 and D), are depicted along with the location of TBP, Taf4, 5 and 12. Taf5 and the histone-fold Tafs, including Taf4 and Taf12, are present in two copies in yeast TFIID, forming a crescent-shaped complex with two-fold symmetry. b, Negatively stained structure of the TFIID-Rap1 complex. The additional density corresponding to Rap1 is colored in red according to difference maps shown in Supplementary Fig. 5a. c, Cryo-EM model of the unstained TFIID-TFIIA-DNA complex formed between TFIID, TFIIA and the Ad2 MLP. Additional densities present in the TFIID-TFIIA-DNA complex are colored. The mass corresponding to TFIIA is represented in blue whereas the density arising in the D lobe ascribed to DNA is represented in green. Original density difference maps are found in Supplementary Fig. 5b.
Figure 2
Figure 2. Structure of the initial TFIID-Activator-Promoter recruitment complex
a, Two different surface views of the Cryo-EM map of Complex I formed upon incubating TFIID, TFIIA, Rap1 and the UASRAP1-PGK1 enhancer-promoter DNA. TFIIA is not detected in Complex I. Densities originating from Rap1 are detected on both sides of lobe B and are colored red. Densities attributed to DNA are colored green in lobes D and C2. b, Enlargement of the area boxed in (a) and fitting of the atomic model of DNA-bound Rap1 DBD into the additional Rap1-density contacting the inner face of lobe B. The rod of additional density protruding towards lobe C2 superimposes to the expected position of Rap1-bound DNA.
Figure 3
Figure 3. Structure of the committed complex
a, Two different surface views of the Cryo-EM map of Complex II formed upon incubating TFIID, TFIIA, Rap1 and UASRAP1-PGK1 enhancer-promoter DNA. The additional densities revealed in Complex II are colored as follows: DNA, TFIIA and Rap1 are depicted in green, violet and red, respectively. b, Enlargement with slight tilting of the area boxed in (a) and fitting of the crystal structure of the TBP-TFIIA and the Rap1-DBD-DNA complexes identifies the bridging density between lobes C1 and B. Note that part of TFIIA is missing in the crystal structure and may affect the fitting c, Comparison of the position of TFIIA between the TFIID-TFIIA-DNA complex (blue) and Complex II (violet) reveals that the position of TFIIA is rotated by 130°. d, Platinum shadowing of spread TFIID-TFIIA-Rap1-DNA complexes showing the formation of a DNA loop in the presence of Rap1.
Figure 4
Figure 4. Model depicting the formation of the activated TFIID complex
a, Binding of Rap1 (red circles) to its specific DNA recognition elements. b, Recruitment of TFIID (yellow) through an interaction with Rap1 and Taf2 (black dot). c, Formation of a DNA loop. d, Recruitment of TFIIA (blue trapezoid) which induces the formation of a protein bridge between lobes B and C1 that locks the DNA loop. e, Model showing the different position of TFIIA in the TFIID-TFIIA-Ad2 MLP DNA complex, which naturally lacks Rap1. The red shape corresponds to TBP while the green triangle represents TAND autoinhibition.
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References

    1. Burley SK, Roeder RG. Biochemistry and structural biology of transcription factor IID (TFIID) Annu Rev Biochem. 1996;65:769–799. - PubMed
    1. Verrijzer CP, Tjian R. TAFs mediate transcriptional activation and promoter selectivity. Trends Biochem Sci. 1996;21:338–342. - PubMed
    1. Jacq X, et al. Human TAFII30 is present in a distinct TFIID complex and is required for transcriptional activation by the estrogen receptor. Cell. 1994;79:107–117. - PubMed
    1. Lieberman PM, Berk AJ. A mechanism for TAFs in transcriptional activation: activation domain enhancement of TFIID-TFIIA--promoter DNA complex formation. Genes Dev. 1994;8:995–1006. - PubMed
    1. Papai G, et al. Mapping the initiator binding Taf2 subunit in the structure of hydrated yeast TFIID. Structure. 2009;17:363–373. - PMC - PubMed

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