TFIIA and the Transactivator Rap1 Cooperate to Commit TFIID for Transcription Initiation

The early steps of activator-dependent transcription in yeast are examined by determining the cryo-EM structures of the transcription activator Rap1 complexed to general transcription factors TFIID and TFIIA and yeast enhancer–promoter DNA. A model is proposed whereby interactions between Rap1 and TFIIA convey activating signals to TFIID, and a Rap1-dependent DNA loop is visualized between the enhancer and the promoter. Here, the early steps of activator-dependent transcription in yeast are examined by using cryo-electron microscopy to study the transcription activator Rap1 in complex with the general transcription factors TFIID and TFIIA and with yeast enhancer–promoter DNA. A model is proposed whereby interactions between Rap1 and TFIIA convey activating signals to TFIID. Moreover, a Rap1-dependent DNA loop is visualized between the enhancer and the promoter. 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.