Transcription apparatus, basal

Chromatin remodeling, transcription factor modification by various enzyme activities, and the communication between the nuclear receptors and the basal transcription apparatus are accomplished by protein-protein interactions with one or more of a class of coregulator molecules. The number of these coregulator molecules now exceeds 100, not counting species variations and splice variants. The first of these to be described was the CREB-binding protein, CBP. CBP, through an amino terminal domain, binds to phosphorylated serine 137 of CREB and mediates transactivation in response to cAMP. It thus is described as a coactivator. CBP and... 

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. 

The TATA box and/or an initiation sequence are structural elements which define a minimal promoter from which in vitro transcription can be initiated. A classical TATA box is often, though not always, ca. 30bp from the transcription start site. The initiation sequence includes sequences in the immediate vicinity of the transcription start site. The TATA box and initiation sequence are sufficient for the formation of a basal transcription apparatus composed of general initiation factors for transcription and RNA polymerase II (see Fig. 1.31). 

Formation of a Basal Transcription Apparatus from General Initiation Factors and RNA Polymerase... 

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. 

It is generally true that that eucaryotic transcriptional activators act via direct or indirect protein-protein contacts with the transcription apparatus. In this context the definition of the transcription apparatus is rather broad it includes the basal apparatus as well as proteins which act as co-activators or mediators (see 1.4.3.2). 

Direct repressors interact with the basal components of the transcription apparatus or with transcriptional activators to inhibit their activity. Specific repressors, analogous to transcriptional activators, are constructed modularly, with a DNA-binding domain and a repressor domain. The repressive character of such domains has been proven in domain swapping experiments. The mechanism of specific repression remains speculative. The following mechanisms are, however, conceivable ... 

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.

RNA polymerases require ancillary factors (proteins) for active transcription these are called transcription factors. The enzyme together with these factors constitutes the basal transcription apparatus. 

TBP bound to the TATA box is the heart of the initiation complex (see Figure 28.19). The surface of the TBP saddle provides docking sites for the binding of other components (Figure 28.21). Additional transcription factors assemble on this nucleus in a defined sequence. TFIIA is recruited, followed by TFIIB and then TFIIF—an ATP-dependent helicase that initially separates the DNA duplex for the polymerase. Finally, RNA polymerase II and then TFIIE join the other factors to form a complex called the basal transcription apparatus. Sometime in the formation of this complex, the carboxyl-terminal domain of the polymerase is phosphorylated on the serine and threonine residues, a process required for successful initiation. The importance of the carboxyl-terminal domain is highlighted by the finding that yeast containing mutant polymerase II with fewer than 10 repeats is not viable. Most of the factors are released before the polymerase leaves the promoter and can then participate in another round of initiation. 

When all these elements are bound to DNA, the basal transcription apparatus complex is formed and can transcribe DNA slowly. Other factors are required for fast, efficient mRNA synthesis. 

Promotor selection, binding of basal initiation factors Binding of the RNA polymerase II Formation of a basal transcription apparatus... 

Mediators include proteins which are organized in multiprotein complexes as a conserved interface between the gene-specific transcription activators and the basal transcription apparatus. They transduce positive or negative regulatory information from promotors or enhancers to RNA polymerase II, modulating its activity. Mediators include, among others, the SRB proteins (see Section 1.4.3.3). A distinct mediator complex from yeast has been described which comprises 20 proteins and is found either in... 

The trans-activating domains of transcriptional activators are also common substrates for phosphorylation by protein kinases. The detailed mechanism by which the phosphorylation affects the interactions with the basal transcription apparatus is known in very few cases. The reason for this is the difficulty of identifying the specific interaction partner in the complex transcription apparatus. 

Fig. 4.11 Model of repression and activation of T3R. In the absence of the T3 hormone, a hetero-dimeric RXR-T3R receptor is bound at the T3-re-sponsive element,TRE, establishing a basal repressed state. The repressed state is maintained by recruitment of corepressor complexes containing histone deacetylase activity. X refers to potential unidentified cofactors (possibly chromatin remodeling complexes or SRBs) which help to keep the promotor-bound basal transcription apparatus in...

In the course of p53 activation, numerous specific protein-protein interactions are engaged to perform the growth-controlling and pro-apoptotic functions of p53. Of these, the interaction with the MDM2 protein stands out, as discussed above. Other important protein-protein interactions include the binding of p53 to components of the basal transcription apparatus, e. g., the TFIIH p62 subunit, interaction with proteins of nucleotide excision repair (XPB, XPD), and the interaction with transcriptional coactivators. 

Fig. 14.7. Transcription apparatus. The TATA-binding protein (TBP), a component of TFIID, binds to the TATA box. Transcription factors TFII A and B bind to TBP. RNA polymerase binds, then TFII E, F, and H bind. This complex can transcribe at a basal level. Some coactivator proteins are present as a component of TFIID, and these can bind to other regulatory DNA binding proteins (called specific transcription factors or transcriptional activators).

Describe the role of TATA-box-binding protein (TBP, TFIID) in forming the basal transcription apparatus. What properties does TBP confer on this apparatus ... 

Finally, the third module is the basal promoter, which in this case binds the a -RNAP holoenzyme complex. This module is responsible for integrating all the inputs thereby generating a particular expression pattern at some integrated rate. The integration of the inputs takes place via a sequential kinetic mechanism, whereby the complex binds the promoter, but is unable to initiate expression, and as a result remains paused at the Transcriptional Start Site (TSS). Simultaneously, the rest of the transcription apparatus assembles at the various binding sites on the enhancer. Transcription is facilitated when the upstream assembled driver complex (e.g. NtrC - the driver (Amit et al. 2011)) loops and makes directs contact with the poised o -RNAP complex. The driver... 

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