Complex basal transcription

The DNA part of each control module can be divided into three main regions, the core or basal promoter elements, the promoter proximal elements and the distal enhancer elements (Figure 9.1). The best characterized core promoter element is the TATA box, a DNA sequence that is rich in A-T base pairs and located 25 base pairs upstream of the transcription start site. The TATA box is recognized by one of the basal transcription factors, the TATA box-binding protein, TBP, which is part of a multisubunit complex called TFIID. This complex in combination with RNA polymerase 11 and other basal transcription factors such as TFIIA and TFIIB form a preinitiation complex for transcription. 

TFIIA and TFIIB are two basal transcription factors that are involved in the nucleation stages of the preinitiation complex by binding to the TBP-TATA box complex. Crystal structures of the ternary complex TFIIA-TBP-TATA box have been determined by the groups of Paul Sigler, Yale University, and Timothy Richmond, ETH, Zurich, and that of the TFIIB-TBP-TATA box by Stephen Burley and collaborators. The TBP-DNA interactions and the distortions of the DNA structure are essentially the same in these ternary complexes as in the binary TBP-TATA complex. 

Nuclear Receptor Regulation of Hepatic Cytochrome P450 Enzymes. Figure 1 General mechanism for transcriptional activation of CYP genes by xenochemicals that activate their cognate xeno-receptor proteins. In the case of Ah receptor, the receptor s heterodimerization partner is Arnt, whereas in the case of the nuclear receptors CAR, PXR, and PPARa, the heterodimerization partner is RXR. The coactivator and basal transcription factor complexes shown are each comprised of a large number of protein components. 

This early biological result spurred a variety of biochemical studies of the interactions of various polyamides with the basal transcription machinery and TE-DNA complexes. Two studies have used promoter scanning to identify sites where polyamide binding inhibits transcription [64, 65]. The method uses a series of DNA constructs with designed polyamide binding sites at varying distances from... 

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.

Figure 37-10. Two models for assembly of the active transcription complex and for how activators and coactivators might enhance transcription. Shown here as a small oval is TBP, which contains TFIID, a large oval that contains all the components of the basal transcription complex illustrated in Figure 37-9 (ie, RNAPII andTFIIA,TFIIB, TFIIE,TFIIF, and TFIIFI). Panel A The basal transcription complex is assembled on the promoter after the TBP subunit of TFIID is bound to the TATA box. Several TAFs (coactivators) are associated with TBP. In this example, a transcription activator, CTF, is shown bound to the CAAT box, forming a loop complex by interacting with a TAF bound to TBP. Panel B The recruitment model. The transcription activator CTF binds to the CAAT box and interacts with a coactivator (TAF in this case). This allows for an interaction with the preformed TBP-basal transcription complex. TBP can now bind to the TATA box, and the assembled complex is fully active.

Work by facilitating binding of the basal transcription complex to the promoter... 

Figure 39-17. Proteins that regulate transcription have several domains. This hypothetical transcription factor has a DNA-binding domain (DBD) that is distinct from a ligand-binding domain (LBD) and several activation domains (ADs) (1-4). Other proteins may lack the DBD or LBD and all may have variable numbers of domains that contact other proteins, including co-regulators and those of the basal transcription complex (see also Chapters 42 and 43).

Figure 43-11. The hormone response transcription unit. The hormone response transcription unit is an assembly of DNA elements and bound proteins that interact, through protein-protein interactions, with a number of coactivator or corepressor molecules. An essential component is the hormone response element which binds the ligand (A)-bound receptor (R). Also Important are the accessory factor elements (AFEs) with bound transcription factors. More than two dozen of these accessory factors (AFs), which are often members of the nuclear receptor superfamily, have been linked to hormone effects on transcription. The AFs can interact with each other, with the liganded nuclear receptors, or with coregulators. These components communicate with the basal transcription complex through a coregulator complex that can consist of one or more members of the pi 60, corepressor, mediator-related, or CBP/p300 families (see Table 43-6).

A small number of proteins, including NCoR and SMRT, comprise the corepressor family. They function, at least in part, as described in Figure 43-2. Another family includes the TRAPs, DRIPs, and ARC (Table 43-6). These so-called mediator-related proteins range in size from 80 kDa to 240 kDa and are thought to be involved in linking the nuclear receptor-coactivator complex to RNA polymerase II and the other components of the basal transcription apparatus. 

In eukaryotes, general transcription factors must bind to the promoter to allow RNA polymerase II to bind and form the initiation complex at the start site for transcription. General manscription factors are common to most genes. The general transcription factor TFIID (the TATA fector) must bind to the TATA box before RNA polymerase II can bind. Other examples delude SP-1 and NF-.l that modulate basal transcription of many genes. 

In vitro interactions between HMG proteins and the basal transcription machinery have also been reported. Human HMGBl binds to the TATA-box binding protein (TBP) and interferes with the normal binding of TFIIB in the preinitiation complex [154,155], thereby inhibiting TBP function both HMGBl and TFIIB independently enhance binding of TBP to TATA-box DNA [154]. Similarly, Nhp6ap promotes the formation of a complex with TBP and TFIIA at the TATA... 

In the resting state, the lysine residues in the N-terminal tail of the histones (see p. 238) are not acetylated. In this state, which can be produced by histone deacetylases [1], the nucleosomes are stable. It is only the interaction of activator and regulator proteins with their control elements that allows the binding of coactivator complexes that have histone acetylase activity [2]. They acetylate the histone tails and thereby loosen the nu-cleosome structure suf ciently for the basal transcription complex to form. 

This consists of DNA-dependent RNA polymerase II and basal transcription factors (TFIIX, X = A - H). First, the basal factor TFIID binds to the promoter. TFIID, a large complex of numerous proteins, contains TATA boxbinding protein (TBP) and so-called TAFs (TBP-associated factors). The polymerase is attached to this core with the help of TFIIB. Before transcription starts, additional TFs have to bind, including TFIIH, which has heli-case activity and separates the two strands of DNA during elongation. In all, some 35 differ-... 

Examples of co-activators are the steroid receptor co-activator (SRC) family [48] and the components of the mammalian mediator complex, which possesses chromatin remodelling ability and tethers activated steroid hormone receptors to the basal transcription machinery [49]. Additional co-... 

In contrast to the procaryotes, where the o -holoenzyme of the RNA polymerase can initiate transcription without the aid of accessory factors, the eucaryotic RNA polymerase requires the help of numerous proteins to begin transcription. These proteins are termed basal or general initiation factors of transcription. Together with RNA polymerase II, they participate in the basal transcription apparatus. The various components must associate in a defined order for the formation of a transcription-competent complex, from which a low level of transcription is possible. An increase in the basal transcriptional level requires the effect of specific transcriptional activators, which bind cognate DNA sequences at a variable distance from the promoter. The transcriptional activators themselves require the aid of further protein factors, known as coactivators (see 1.4.3.2), in order to attain full stimulatory activity. 

Fig. 1.32. Phosphorylation of the C-terminal domain of RNA polymerase II and the beginning of transcription. The transition from the initiation complex to actual begin of transcription is regulated via phosphorylation of the C-terminal domain (CTD) of RNA polymerase II. In the above model it is assumed that initially a complex is formed between TFIID and a holoenzyme of RNA polymerase consisting of RNA polymerase II and associated factors (mediators, SRB proteins) and the basal transcription factors. Phosphorylation of the C-terminal domain effects the dissociation of the RNA polymerase from the initation complex and the transition to the elongation phase. A protein kinase, which is part of TFIIH, is responsible for the phosphorylation. The nature of the signal that induces phosphorylation of RNA polymerase II remains unknown. SRB suppressor of RNA polymerase B. After Koleske and Young (1995).

The formation of an active, regulation-competent initiation complex for transcription in eucaryotes demands the concerted action of a large number of proteins. It is estimated that more than 50 different proteins participate in the initiation of transcription in eucaryotes. The basal transcription complex, consisting of the general initiation factors, as well as RNA polymerase 11, allows only for a slow transcription rate. For a regulated acceleration of this low transcription rate it is necessary to have - apart from the regulatory DNA-binding proteins - mediation by further co-activator proteins. 

The TAFs are components of TFIID (see table 1.1) and are required for a regulated transcription (review Verriijzer and Tijan 1996, Bmley and Roeder, 1996 ). Thus, the stimulation of transcription by the transcriptional activators Spl and NTF-1 depends upon the presence of specific TAFs in the TFllD complex. The TAFs mediate interactions between the transcriptional activators and the TFllD complex in many cases direct protein-protein interactions could be demonstrated between the activators and TAFs. Some of the TAFs possess additional enzymatic activities which allow them to participate in the regulation of transcription. By this token, the histone acetylase and protein kinase activity of TAFn250 is ascribed a regulatory function in the remodeling of chromatin and in the control of the activity of the basal transcription factors. 

An example of a negative cofactor is the NC2 complex, which can repress the basal transcription level. The NC2 complex consists of two subimits, both displaying homology to the histone proteins. The repressive fimction of NC2 is due to its competition with TFIIB and TFIIA for the promoter binding site, thus blocking formation of the pre-initiation complex. 

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. 

Fig. 1.40. Model of repression and activation of transcription. The figure illustrates various mechanisms of repression of transcription, a) genes are in a generally repressed states in inactive chromatin. In a first phase of activation the chromatin is restrnctured. b) The promoter is now accessible for the binding of the basal transcription factors and for RNA polymerase II. c) An initiation complex is formed that contains the central components of the transcription apparatns, bnt which enables transcription only at a low rate, d) the binding of repressors to the transcription initiation complex can prevent fnrther activation of transcription at this step, e) the binding of transcription activators to their DNA elements leads to activation of transcription, f) an active repression is affected by proteins that bind seqnence specifically to DNA elements and in their DNA-bound form inhibit the transcritption preventing interactions with the transcription apparatus.

Mediators and coactivators. Transcriptional activators that act in a crude cell-free system often do not function with purified DNA, RNA polymerase, and the basal transcription factors as indicated in Eq. 28-5. Studies with yeast, Drosophila, and human cells revealed that additional large multisubunit complexes known as mediators are needed 272/346-348 A yeast mediator complex consists of 20 subunits.349-350b Many activator proteins bind to the DNA sequences known as enchancers, discussed in the next section. Mediator complexes may also interact with enhancer-bound activators. Individual proteins, such as the TAF subunits, that bind to and cooperate with activator proteins are often called coactivators.351... 

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