Core promoter-binding factor

A core promoter-binding factor (CPBF) has been described in rats. This is a dimeric factor that binds to the rDNA promoter sequences and increases the rate of transcription initiation (Liu and Jacob, 1994). CPBF appears to exert its function by physically interacting with EjBF/Ku at the rDNA promoter (Liu and Jacob, 1994 Niu et al., 1995). CPBF is highly... 

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. 

The general transcription factor TFllD is believed to be the key link between specific transcription factors and the general preinitiation complex. However, the purification and molecular characterization of TFllD from higher eucaryotes have been hampered by its instability and heterogeneity. All preparations of TFllD contain the TATA box-binding protein in combination with a variety of different proteins called TBP-associated factors, TAFs. When the preinitiation complex has been assembled, strand separation of the DNA duplex occurs at the transcription start site, and RNA polymerase II is released from the promoter to initiate transcription. However, TFIID can remain bound to the core promoter and support rapid reinitiation of transcription by recruiting another molecule of RNA polymerase. 

General or basic transcription factors are required for every gene to allow the proper recruitment of RNA polymerases to ensure transcriptional activity. They bind to core promoters in the vicinity of transcriptional start sites in a sequential manner. 

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. 

The rRNA promoter consists of a core element which straddles the transcriptional start site (designated as position +1) from residues -31 to +6 plus an upstream control element (UCE) about 50-80 bp in size and located about 100 bp upstream from the start site (i.e. at position -100 Fig. 4b). A transcription factor called upstream binding factor (UBF) binds both to the UCE as well as to a region next to and overlapping with the core element. Interestingly, TATA box binding protein (TBP see Topic G6), also binds to the rRNA promoter (in fact, TBP is required for initiation by all three eukaryotic RNA polymerases). The UBF and TBP transcription factors interact with each other and with RNA Pol I to form a transcription initiation complex. The RNA Pol I then transcribes... 

The 5 end of MT-1 and MT-2 genes possess a TATA box, or core promoter element and numerous response elements that confer metal inducibility on the MT gene promoter (Figure 21.8). Some of these response elements such as API and AP2 in humans and in mouse, the antioxidant response element (ARE) and upstream stimulatory factor (USF) provide putative binding sites for MT transcription factors. The most common of these cis-acting proximal elements are the metal responsive elements (MREs), motifs that are conserved across vertebrate and invertebrate species. Multiple copies of MREs exist in the MT promoter region and act syner-gistically to enhance activity. 

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... 

A simplified diagram of transcription is shown here. Double-stranded DNA (dsDNA) is shown as a long rectangle. RNA polymerase binds to a region of DNA called a core promoter The core promoter consists of all the DNA between the TATA sequence and the transcription start site. The core promoter is a short stretch of DNA that serves to bind and orient RNA polymerase, and the basal transcription factors. The TATA sequence, which is composed of only four nucleotides T A, T, and A), usually occurs about 25 base pairs upstream of the transcription start site. The TATA-binding protein is a special protein that binds to the TATA sequence prior to initiating transcription. 

The region immediately upstream of the core promoter is called the proximal promoter and usually contains a number of transcription factor binding sites responsible for the assembly of an activation complex. This complex in turn recruits the polymerase complex. It is generally accepted that most proximal promoter elements are located within a stretch of about 250-500 nucleotides upstream of the actual transcription start site (TSS). 

Lagrange, T., Kapanidis, A. N., Tang, H., Reinberg, D., and Ebright, R. H. (1998). New core promoter element in RNA polymerase II dependent transcription sequence specific DNA binding by transcription factor IIB. Genes Dev. 12(1), 34-44. 

Promoter analysis indicates a 39-bp core promoter, containing TATA and inihator elements that control transcription. Binding of the tran-sciiphon factor NF-E2 is critical both for altera-hon of the nucleosomal structure and for activa-hon of the P450 5A1 promoter [1668]. 

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