Upstream promoter sequence

Promoter regions (switch on transcription) Upstream promoter sequence CAAT followed by Core (or Basal) promoter TATA (Hogness box) Sequence TTGACA (-35) followed by TATAAT (-10 or Pribnow box) are upstream of the transcription start (+1)... 

Ellis, J.G., Llewellyn, D.J., Dennis, E.S. Peacock, W.J. (1987). Maize Adh-1 promoter sequences control anaerobic regulation addition of upstream promoter elements from constitutive genes is necessary for expression in tobacco. EM BO Journal, 6, 11-16. 

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... 

Activator proteins (and a few repressors) are important in eukaryotes, as they are in prokaryotes. The DNA sequences to which activator proteins bind in eiikaryotic DNA are called response elements. A few response elements are located within the promoter region (upstream promoter elements [UPE]), but most are outside the promoter and often clustered to form an enhancer region that allows control of gene expression by multiple signals (Figure 1-5-4). 

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

An increase in the basal transcription activity originating from the promoter requires regulatory DNA sequences. These sequences can be proximally or distaUy located and serve as binding sites for transcriptional activators. The cis-acting DNA elements can be found near the promoter in either orientation. They are often termed upstream activating sequences" (UAS). Regulatory sequences can also be located far from the promoter. Their effect is independent of their orientation and they are known as enhancers. 

Fig. 1.30. Structure of a typical eucaryotic transcription start site. Enhancer elements and UAS elements (UAS upstream activating sequences) are binding sites for positive and negative regulatory DNA-binding proteins. The TATA box is the binding site for the TATA box binding protein (TBP) and serves to position the RNA polymerase holoenzyme on the promoter. For promoters that do not possess a TATA box, this function is fulfilled by an initiator region.

FIGURE 28-2 Consensus sequence for many E. coli promoters. Most base substitutions in the -10 and —35 regions have a negative effect on promoter function. Some promoters also include the UP (upstream promoter) element (see Fig. 26-5). By convention, DNA sequences... 

Promoter sequences. In 1975, Pribnow pointed out46 that a series of six known promoters had a conserved 7-base sequence beginning six nucleotides upstream from the initiation site for transcription. Although this sequence varies somewhat from one promoter to another, it has been found in hundreds of E. coli promoters. This is called the -10 region, the Pribnow sequence, or Pribnow box (the last in recognition of the fact that people like to draw boxes around these special sequences). A typical 6-base consensus Pribnow sequence is 5-TATAAT as written for the coding strand, whose sequence corresponds to that of the rnRNA. Only three of these bases are highly... 

PCR-generated linear DNA template. The template contains a T7 promoter sequence immediately upstream to the RNA sequence, the first nucleotide after the T7 promoter (+1) is changed to G to improve transcription yield and the last two nucleotides of the template are methylated at 2 -0 position to reduce 3 -end heterogeneity of the transcribed RNA. The transcript is purified either on a 5% denaturing PAGE or by the MEGA-clear kit (Ambion) and dissolved in CE buffer at stock concentrations of 10-50 fiM. 

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