Mechanism of assembly of the RNA polymerase II preinitiation complex: Transcription factors δ and ε promote stable binding of the transcription apparatus to the initiator element

Assembly of RNA polymerase II with the core region of TATA box-containing promoters requires the action of the TATA factor and four transcription factors designated α, βγ, δ, and ε, which have each been purified to near homogeneity from rat liver. Evidence from previous studies argues that α and βγ play a crucial role in delivering RNA polymerase II to the promoter (Conaway, R. C., Garrett, K. P., Hanley, J. P., and Conaway, J. W. (1991) Proc. Natl. Acad. Sci. U. S. A. 88, 6205-6209). Here we describe the interaction of transcription factor δ with preinitiation intermediates assembled in the presence of either recombinant yeast TFIID or the high molecular mass, endogenous TATA factor τ from rat liver (Conaway, J. W., Hanley, J. P., Garrett, K. P., and Conaway, R. C. (1991) J. Biol. Chem. 266, 7804-7811). Results of template challenge experiments argue that δ enters the preinitiation complex through interactions with multiple components of the transcription apparatus. We observe that, in the presence of recombinant TFIID, 5 interacts stably with the preinitiation complex only in the presence of RNA polymerase II, α, and βγ, whereas, in the presence of τ, δ is capable of interacting stably with the Initial Complex independently of RNA polymerase II. Results of restriction site protection experiments reveal that δ and ε promote binding of the transcription apparatus to the Initiator element and support the model that RNA polymerase II assembles at the core promoter in at least two discrete steps, first "touching down" near the TATA element and finally extending its interaction downstream to encompass the cap site.