Transcription at promoters

RNA polymerases bind to DNA and initiate transcription at promoters (see Fig. 26-5), sites generally found near points at which RNA synthesis begins on the DNA template. The regulation of transcription initiation often entails changes in how RNA polymerase interacts with a promoter. 

Another important coactivator consists of 20 or more polypeptides in a protein complex called mediator (Fig. 28-27) the 20 core polypeptides are highly conserved from fungi to humans. Mediator binds tightly to the carboxyl-terminal domain (CTD) of the largest subunit of Pol II. The mediator complex is required for both basal and regulated transcription at promoters used by Pol II, and it also stimulates the phosphorylation of the CTD by TFIIH. Both mediator and TFIID are required at some promoters. As with TFIID, some DNA-binding transactivators interact with one or more components of the mediator complex. Coactivator complexes function at or near the promoter s TATA box. 

The a 2 P P core of RNA polymerase is unable to start transcription at promoter sites. Rather, the complete a 2 P P <7 holoenzyme is essential for initiation at the correct start site. The c subunit contributes to specific initiation in two ways. First, it decreases the affinity of RNA polymerase for general regions of DNA by a factor oflO". In its absence, the core enzyme binds DNA indiscriminately and tightly. Second, the o subunit enables RNA polymerase to recognize promoter sites. A large fragment of a o subunit was found to have an a helix on its surface this helix has been implicated in... 

EXAMPLE 9.15 How can enhancer sequences influence transcription at promoters that are so far away ... 

Enhancer elements that stimulate transcription in vivo at adjacent promoters are thought to be important in regulation of genes during differentiation. The mechanism by which such an element can enhance transcription at promoters positioned over 1000 base pairs away is not known. Some have suggested that enhancer elements may be sites of entry for pol II, it being subsequently transferred to the ini-... 

DNA-Dependent RNA Polymerase Initiates Transcription at a Distinct Site, the Promoter... 

Katsuhiko, M., Owens, J.T., Belyaeva, T.A., Meares, C.F., Busby, S.J.W., and Ishihama, A. (1997) Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors. PNAS 94, 11274-11278. 

There is a single prokaryotic RNA polymerase that synthesizes all types of RNA in the cell. The core polymerase responsible for making the RNA molecule has the subunit structure Ojpp. A protein factor called sigma (a) is required for the initiation of transcription at a promoter. Sigma factor is released immediately after initiation of transcription. Termination of transcription sometimes requires a protein called rho (p) faaor. This enzyme is inhibited by rifampin. Actinomycin D binds to the DNA preventing transcription. 

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.

TABLE 26-1 Proteins Required for Initiation of Transcription at the RNA Polymerase II (Pol II) Promoters of Eukaryotes... 

Regulation of RNA Polymerase II Activity Regulation of transcription at Pol II promoters is quite elaborate. It involves the interaction of a wide variety of other proteins with the preinitiation complex. Some of these regulatory proteins interact with transcription factors, others with Pol II itself. Many interact through TFIID, a complex of about 12 proteins, including TBP and certain... 

Control by looping. The arabinose utilization operon of E. coli, araBAD, encodes proteins needed for uptake of arabinose and conversion to D-xylulose 5-P. The repressor AraC in the absence of arabinose binds at operator 1 (Oj) to prevent further synthesis of repressor (autorepression) and also at the aral region to repress transcription of operon araBAD. The operator 2 (02) site, which is 211 bp upstream from aral, is also needed for this repression.145-14713 A loop is apparently formed by repressor binding (Fig. 28-7). Binding of arabinose to the repressor converts it into an activator, which stimulates initiation of transcription at the BAD promoter. Further stimulation is provided by the CAP-cAMP complex, which binds next at aral. 

Promoters for RNA Pol I, like those of Pol II, lie upstream of the initiation site for transcription. At least two transcription factors have been identified47 477 478a and vary among species. The human factors bind to a G C-rich DNA sequence in the -45 to... 

Alternative Sigma Factors Trigger Initiation of Transcription at Different Promoters Elongation of the Transcript Termination of Transcription Comparison of Escherichia coli RNA Polymerase with DNA Poll and PolIII... 

Alternative Sigma Factors Trigger Initiation of Transcription at Different Promoters... 

Enhancer. A DNA sequence that can bind protein factors that stimulate transcription at an appreciable distance from the site where it is located. It acts in either orientation and either upstream or downstream from the promoter. 

The methods used for the evaluation of regulation of gene expression are too numerous to be described in detail here. They include Northern analysis to determine levels of a particular mRNA, nuclear run on to determine whether an increase in mRNA is due to an increase in the rate of transcription, and promoter deletion analysis to identify specific elements in the promoter region responsible for the control of expression. Of much current interest is the use of microarrays that permit the study of the expression of hundreds to thousands of genes at the same time. Reverse transcriptase-polymerase chain reaction and RNase protection assay techniques are used to amplify and quantitate mRNAs, while the electrophoretic mobility shift assay is used to measure binding of a transcription factor to its specific DNA consensus sequence. 

In Canton-S strain, desat2 is not transcribed in either sex (Dallerac et al 2000), and the same 16 bp deletion is observed in the 5 -region of the gene. According to the promoter prediction shown in Figure 9.10, this deletion results in a lower probability of transcription at the same site and might be responsible for the lack of transcription of desat2 in Canton-S. 

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