TFIID formation

The sharp bend of DNA at the TATA box induced by TBP binding is favorable for the formation of the complete DNA control module in particular, for the interaction of specific transcription factors with TFIID. Since these factors may bind to DNA several hundred base pairs away from the TATA box, and at the same time may interact with TBP through one or several TAFs, there must be several protein-DNA interactions within this module that distort the regular B-DNA structure (see Figure 9.2). The DNA bend caused by the binding of TBP to the TATA box is one important step to bring activators near to the site of action of RNA polymerase. 

Figure 37-9. The eukaryotic basal transcription complex. Formation of the basal transcription complex begins when TFIID binds to the TATA box. It directs the assembly of several other components by protein-DNA and protein-protein interactions. The entire complex spans DNA from position -30 to +30 relative to the initiation site (+1, marked by bent arrow). The atomic level, x-ray-derived structures of RNA polymerase II alone and ofTBP bound to TATA promoter DNA in the presence of either TFIIB or TFIIA have all been solved at 3 A resolution. The structure of TFIID complexes have been determined by electron microscopy at 30 A resolution. Thus, the molecular structures of the transcription machinery are beginning to be elucidated. Much of this structural information is consistent with the models presented here.

The formation of the PIC described above is based on the sequential addition of purified components in in vitro experiments. An essential feature of this model is that the assembly takes place on the DNA template. Accordingly, transcription activators, which have autonomous DNA binding and activation domains (see Chapter 39), are thought to function by stimulating either PIC formation or PIC function. The TAF coactivators are viewed as bridging factors that communicate between the upstream activators, the proteins associated with pol II, or the many other components of TFIID. This view, which assumes that there is stepwise assembly of the PIC—promoted by various interactions between activators, coactivators, and PIC components— is illustrated in panel A of Figure 37-10. This model was supported by observations that many of these proteins could indeed bind to one another in vitro. 

TFIIA and TFIIB support TFIID in the formation of a stable complex with the promotor. TFllB is necessary for the downstream selection of the start site for RNA polymerase 11. Interactions with TFllB ensure correct positioning of the RNA polymerase 11 on the promoter. Crystal structures have been solved for several of the intermediates of the pre-initiation complex (review Sokolev and Burley, 1997), showing, for example, that TBP affects a predominant kink in the DNA (see Fig. 1.16). TFIIB binds to the TBP-DNA complex, contacting both TBP and the DNA. 

In one model it is assumed that transcriptional activators and coactivators increase the efficiency of formation of the pre-initiation complex. This function includes a restructuring of chromatin at the transcription start site. In this context the formation of the TFIID complex at the promoter plays an important role. 

Direct inhibition of the formation of a pre-initiation complex complexation of basal transcription factors, such as TFIID or TFIIB, or competition with TFIIB for binding to the promoter. An example for this type of repression is the negative cofactor NC2 (see 1.4.3.2). Transcription repression can also result from phosphorylation of the basal transcription factors. By this token, the repression of transcription observed during mitosis is attributed to the hyperphosphorylation of TBP and TAFs. 

Retention of transcription factors in mitotic chromosomes could provide one component of this molecular memory. Immunocytochemical and subcellular fraction of mitotic Hela cells indicated that some TFIID remained associated with mitotic chromatin (Segil et al., 1996). Thus, upon entry into interphase, TFIID could nucleate the formation of a productive transcription complex for a gene expressed in G2 of the prior cell cycle. The retention of other transcription factors Or enhancer proteins could promote the same effect. 

The ability of the histone-like TAFs to form an octamer-like structure raises the possibility that the TAF octamer may wrap promoter DNA in a manner similar to the nucleosome (Hoffmann et al., 1997 Oelgeschlager et al., 1996). This hypothesis is supported by the resemblance of DNase I footprinting patterns of TFIID on the Adenovirus Major Late (AdML) promoter to those of nucleosomal DNA. However, the arginine side chains in histones that form primary contacts with DNA are not conserved in TAFs (Luger et al., 1997). Therefore, the histone fold domain interaction may be used only for the formation of a compact structure and is not necessarily involved in DNA wrapping. 

---