Proximal promoter element

Archaebacterial RNA polymerases are very different from their eubacterial counterparts and more closely resemble eukaryotic enzymes both in their subunit complexity and in their amino acid sequences (for review, see Puehler et al., 1989). This view is also reflected in the diversity of the DNA sequences that are used by the transcription apparatus as signals for initiation of transcription, namely, the promoters. Many attempts were made to identify a consensus promoter structure (Zillig et al., 1988). However, as more genes are isolated and characterized, the picture becomes less coherent. Earlier identification of two upstream sequences, box A and box B, located around positions — 30 and + 1, respectively, gave way to two elements —DPE (distal promoter element) and PPE (proximal promoter element)—located - 38 to - 25 and — 11 to — 2, respectively (Reiter et al., 1990). The DPE encompasses the box A sequence TTTA(A or T)A, but the PPE sequence seems to depend more on an (A + T)-rich sequence rather than on a specific DNA sequence. 

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). 

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. 

Figure 9.1 The transcriptional elements of a eucaryotic structural gene extend over a large region of DNA. The regulatory sequences can be divided into three main regions (1) the basal promoter elements such as the TATA box, (2) the promoter proximal elements close to the initiation site, and (3) distal enhancer elements far from the initiation site.

A third class of sequence elements can either increase or decrease the rate of transcription initiation of eukaryotic genes. These elements are called either enhancers or repressors (or silencers), depending on which effect they have. They have been found in a variety of locations both upstream and downstream of the transcription start site and even within the transcribed portions of some genes. In contrast to proximal and upstream promoter elements, enhancers and silencers can exert their effects when located hundreds or even thousands of bases away from transcription units located on the same chromosome. Surprisingly, enhancers and silencers can function in an orientation-independent fashion. Literally hundreds of these elements have been described. In some cases, the sequence requirements for binding are rigidly constrained in others, considerable sequence variation is... 

Within the proximal promoter are found five sequence elements that are conserved between D. melanogaster and D. virilis (Scholnick et al., 1986) (Fig. 5). The 16-bp element I sequence is perfectly conserved between D. melanogaster and D. virilis (Bray and Hirsh, 1986). Inactivation of element I by deletion or point mutation leads to a selective loss of Ddc expression within the CNS (Scholnick et al., 1986 Bray et al., 1988) (Fig. 6A), without significantly affecting hypodermal Ddc expression. This demonstrates that element I is required specifically for expression of Ddc within the CNS. 

ADH6 was discovered by nucleotide cross-hybridization, and has not yet been demonstrated as a functional protein. The mRNA is found in liver (both adult and fetal) and stomach. ADH6 has a fully functional promoter, active in both hepatoma cells and fibroblasts [37]. There are several positive cis-acting elements in the proximal promoter, several of which are bound by C/EBP. There is a compound cell-specific regulatory element about 2 kb upstream, that is a positive element in the hepatoma cells and a negative element in fibroblasts [23]. 

Only the proximity of the upstream promoter element to the -25 sequence distinguishes it from an enhancer. Upstream promoter elements include ... 

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. 

Elements independent of operation and position (in contrast to proximal promoter... 

Element Klundert, F.A., Jansen, H.J., and Bloemendal, H A proximal promoter... 

The promoter of STSSia I (GD3-synthase, STII), which has attracted much more attention than have other promoters of the ganglioside synthase genes, has been cloned from rat [103], mouse [104] and human [105]. The promoter of all three species is TATA-less and does not possess known core- promoter elements, including the initiator (INR), the downstream promoter (DPE), the TFIIB recognition elements (BRE), and the motif ten element (MTE). Similar to other TATA-less promoters, it has a high GC content and is enriched in Spl-bind-ing sites. The proximal promoter region is defined within 500 or 700 bp upstream of the ATG... 

The tissue-selective expression of several CYP genes in the respiratory tract has been explored in order to identify mechanisms of regulation, primarily through the use of animal models. For CYP2A, a nuclear factor I-like element (called NPTA element) is present in the proximal promoter region it is conserved in rodent and... 

The regulation of transcription can simply be viewed as correctly localizing RNA polymerase to the appropriate position to initiate transcription. From this vantage, the function of promoters (elements located proximal to the transcription start site) and enhancers (elements located more distal to the transcription start site) are essentially the same in that they recruit in a cooperative fashion and localize RNA polymerase to its initiation site. In the absence of these elements, the binding of RNA polymerase to DNA is both of low-affinity and promiscuous. Another function proposed for enhancers is to relieve chromatin-mediated repression of a weak promoter (Majumder and DePamphilis, 1995). It should be noted that these two functions are not mutually exclusive. 

Enhancer-dependent expression is observed following transplantation of an injected pronucleus into a two-cell blastomere (Henery et al., 1995) (Figure 4). The first mitosis—and concomitant loss of the plasmid from the injected pronucleus—was circumvented by the transplantation procedure and hence cannot account for the enhancer requirement observed in the two-cell embryo. The luciferase reporter gene is driven by the / promoter, which has two Spl binding sites (termed the proximal and distal sites)—a CAAT box binding site that binds CTF and a TATA box that binds TBP. Analysis of the expression of a set of linker scanning mutations that inactivated each of these sites without altering the distances between each of the promoter elements revealed that each mutation had the same relative effect on tk... 

In the rat Mrp2 gene, a single ER8 motif in the proximal promoter region at around —0.4 kb was identified, which mediates induction by PXR and CAR [99], Electrophoretic mobility shift assays showed that PXR and CAR bound to this element... 

A FIGURE 11-12 General pattern of control elements that regulate gene expression in multicellular eukaryotes and yeast, (a) Genes of multicellular organisms contain both promoter-proximal elements and enhancers, as well as a TATA box or other promoter element. The promoter elements position RNA polymerase II to initiate transcription at the start site and influence the rate of transcription. Enhancers may be either... 

Transcription factors, which stimulate or repress transcription, bind to promoter-proximal regulatory elements and enhancers in eukaryotic DNA. 

---