Transcription promoter structure

Busby S, Ebright RH Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 1994 79 ... 

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. 

We then turn to transcription in eukaryotes, beginning with promoter structure and the transcription-factor proteins that regulate promoter activity. A distinctive feature of eukaryotic DNA templates is the presence of enhancer sequences that... 

The chemistry of transcription in eukaryotes is the same as in prokaryotes. However, the promoter structure and the mechanism for initiation are strikingly different. 

Gilinger, G., Alwine, J. C. (1993) Transcriptional activation by simian virus-40 large T-Antigen - requirements for simple promoter structures containing either TATA or initiator elements with variable upstream factor binding sites. J Virol 67, 6682-6688. 

Cramer, P., Pesce, C. G., Baralle, F. E., Kornblihtt, A. R. (1997) Functional association between promoter structure and transcript alternative splicing. Proc Natl Acad Sci USA 94, 11456-11460. 

Transcription initiation rates - In E. coli, rates of transcription initiation vary enormously—from about one initiation every 10 seconds for some genes to as infrequently as once per generation (30 to 60 minutes) for others. Because all genes in bacteria are transcribed by the same core enzyme, variations in promoter structure must be largely responsible for the great variation in the frequency of initiation. Variations in promoter structure represent a simple way for the cell to vary rates of transcription from different genes. 

TFIID is the only GTF with intrinsic DNA sequence specificity and is responsible for nucleating the assembly of Pol II preinitiation complex at core promoters. The interaction between TFIID and core promoter is mediated by the affinity of several specific subunits for distinct core promoter elements (Verrijzer and Tjian, 1996). Because TBP functions in transcription by all three nuclear RNA polymerases, these specific interactions help TFIID to distinguish different promoter structures and properly direct Pol II transcription machinery to its target genes. 

Pribnow box a sequence of seven nucleotide pairs, which is the same or very similar in all promoters. It is located five to seven nucleotide pairs from the initiation point of RNA transcription. The structure of the P.b is ... 

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.

In rarer cases the ODNs also prevent normal gene transcription by directly forming triplex-helix structures with target DNA. This does not destroy a gene but prevents its unwinding or its binding to a gene promoter. 

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