Downstream promoter element

A small number of genes lack a TATA box. In such instances, two additional cis elements, an initiator sequence (Inr) and the so-called downstream promoter element (DPE), direct RNA polymerase II to the promoter and in so doing provide basal transcription starting from the correct site. The Inr element spans the start... 

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... 

The holoenzyme binds to a promoter region about 40-60 bp in size and then initiates transcription a short distance downstream (i.e. 3 to the promoter). Within the promoter lie two 6-bp sequences that are particularly important for promoter function and which are therefore highly conserved between species. Using the convention of calling the first nucleotide of a transcribed sequence as +1, these two promoter elements lie at positions -10 and -35, that is about 10 and 35 bp, respectively, upstream of where transcription will begin (Fig. 1). 

T.W. Burke, P.J. Willy, A.K. Kutach, J.E. Butler and J.T. Kadonaga. The DPE, a conserved downstream core promoter element that is functionally analogous to the TATA box. Cold Spring Harb. Symp. Quant. Biol. 63 (1998) 75-82. 

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... 

More complex transcriptional regulation. Like prokaryotes, eukaryotes rely on conserved sequences in DN A to regulate the initiation of transcription. But prokaryotes have only three promoter elements (the —10. -33. and UP elements), whereas eukaryotes use a variety of types of promoter elements, each identified by its own conserved sequence. Not all possible types will he present together in the same promoter. n eukaryotes, elements that regulate transcription can be found at a variety of locations in DNA, upstream or downstream of the start site and sometimes at distances much farther from the start site than in prokaryotes. For example, enhancer elements located on DNA far from the start site increase the promoter activity of specific genes. 

Figure 29.17 Common eukaryotic promoter elements. Each eukaryotic RNA polymerase recognizes a set of promoier elements—sequences in DNA that promote transcription 1 he KNA polymerase I promoter consists of a ribosomal initator (rlnr) and an upstream promoter element (UPE). Tfie RNA polymerase II promotei likewise includes an initator element (Inr) and may also include either a TATA box or a downstream promoter dement (DPE), Separate from the promoter region, enhancer dements bind specific transcription factors. RNA polymerase III promoters consist of conserved sequences that lie within the transcribed genes.

A third element, the doumsheam core promoter element (DPE). is com monly found in conjunction with the Inr in transcripts that lack theT.Al A box. In contrast with the TA FA box, the DPE is found downstream ot the start site, between positions +28 and +32. 

The core promoter module can be defined functionally by its capability to assemble the transcription initiation complex (see Figure 4.3) and orient it specifically towards the TSS of the promoter [13], defining the exact location of the TSS. Various combinations of about four distinguishable core promoter elements that constitute a general core promoter can achieve this. This module includes the TATA box, the initiator region (INR), an upstream activating element, and a downstream element. (The TATA box is a basic... 

A cloning vector is also cut with the same pair of restriction endonucleases downstream of the promoter element (p) (see Figure 3.5). In cloning vector, pDNA sense strand is dark grey complementary strand is in light grey. In heterologous DNA, sense strand is in red complementary strand is in yellow. 

This relieves phosphatase inhibition of the kinase, thereby enabling autophosphorylation and thus activation of the kinase domain. Active SnRK2 kinases subsequently activate further downstream transcription factors (DTFs), thereby starting transcription at ABA-responsive promoter elements (ABREs). 

The promoter composition and organization of eukaryotic polymerases are quite specific for each polymerase. The promoters of rRNA genes contain a core and an upstream control element which is needed for high promoter activity. Two ancillary factors, UBH and SLl, bind to these sequences. Although SLl binds only after UBFl in a cooperative fashion, SLl is a a-factor with four proteins among which TBP is also required for initiation by the other polymerases. Pol 1 is akin to Pol ill in that it utilizes both upstream and downstream promoters. There are two types of internal promoters with distinct sequence boxes. One transcription factor (TFin B) is required for initiation of RNA synthesis by Pol in. Other factors (TFin A and TFIII C) help TFin B bind to the right location and... 

Burke T.W. and Kadonaga J.T. 1997. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev. 11 3020-3031. Heiermann R. and Pongs 0.1985. In vitro transcription with extracts of nuclei of Drosophila embryos. 

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