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Eukaryotic promoters are somewhat similar to prokaryotic promoters; both are regions of DNA at the beginnings of genes with signals that allow RNA polymerase to attach and begin transcription. In eukaryotes, however, more proteins are involved in promoter recognition, and more proteins are involved in the control of transcription, many recognizing signals thousands of base pairs away. We discuss these control processes in eukaryotes in chapter 16. All three eukaryotic RNA polymerases (I, II, and III) recognize a seven-base sequence, TATAAAA, located at about 25 on the promoter DNA. It is similar to the 10 sequence in prokaryotes and is called the TATA box (or Hogness box after its discoverer, D. Hogness). Since RNA polymerase II transcribes most of the genes in eukaryotes, we turn our attention speci cally to it. Among the large number of promoters that have been sequenced, a few lack the TATA box, yet are still transcribed. Transcription initiation in these promoters appears to be controlled by a CT-rich area, called the initiator element (Inr), at 1 of the transcript (close to the transcription start site), coupled with a downstream promoter element (DPE) at about 28 to 34 of the transcript. In TATA-less promoters, a protein called TFIID requires both these elements to bind. The initiator element has a consensus sequence of TCA(G or T)T(T or C), and the downstream promoter element has the consensus sequence of (A or G)G(A or T)CGTG. We will concentrate on RNA polymerase II genes with TATA boxes. Yeast RNA polymerase II is a protein of twelve subunits. This enzyme cannot locate promoters or attach to DNA in a stable fashion. To attach at the beginnings of genes, RNA polymerase II must interact with several proteins called general transcription factors. In eukaryotes, general transcription factors are named after the polymerase they work with. Thus, the transcription factor that recognizes the TATA box for polymerase II genes is called TFIID (D being the fourth letter of the alphabet for the fourth transcription factor so named). TFIID is composed of one
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Figure 10.23 Molecular space- lling model of a yeast TATAbinding protein attached to a TATA box on the DNA. The DNA sugar-phosphate backbone is green and the bases are yellow. The protein has twofold symmetry (red and blue). Note the bending of the DNA through 80 degrees, which also opens up the minor groove of the DNA. The upper white atoms are the N-terminus of the TATA-binding protein; the lower white atoms are the rst base pair at which transcription begins. (Courtesy of
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J. L. Kim and S. K. Burley. From J. L. Kim, J. H. Geiger, S. Hahn, and P. B. Sigler, Crystal Structure of a Yeast TBP TATA-box Complex. Nature 365 (6446): 520 27, Oct. 7, 1993. Macmillan Magazines, Ltd. Figure adapted from the work of S. K. Burley.)
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subunit that recognizes the TATA sequence, called TATAbinding protein (TBP), and up to a dozen other proteins called TBP-associated factors (TAFs), which recognize the initiator element, when present, and aid in regulating transcription. TFIID is, in essence, similar to the sigma factors of prokaryotic RNA polymerase. One interesting aspect of the binding of TBP is that it causes a signi cant bending and opening of the DNA ( g. 10.23).This bending may be an important signal for other binding proteins. Once TFIID binds to the TATA box, a cascade of recruitment (binding) of other transcription factors takes place. Transcription factors IIA, IIB, and IIF bind, as does RNA polymerase II in an unphosphorylated state. Then transcription factors IIE and IIH bind, forming a preinitiation complex (PIC), equivalent to the E. coli holoenzyme ( g. 10.24a). The RNA polymerase II is then phosphorylated, presumably by TFIIH, which is a kinase; at this point, most of the transcription factors drop off, leaving the elongation complex, which carries out a
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