RNA polymerase II promoters

Sequences found in and near some RNA polymerase II promoters. Only the TATA box is represented in many promoters (some promotors lack this sequence). The CAAT box occurs much less frequently, and the GC box has only occasionally been observed. Upstream sites are very common but are not considered to be part of the promoter. 

RNA molecules destined to become mRNA. Polymerase III synthesizes 5S rRNA and the tRNAs. 

The structure of eukaryotic promoters is more complex than that of prokaryotic promoters. DNA sequences, hundreds of base pairs (bp) upstream from the transcription start site, control the rate of initiation. Furthermore, initiation requires numerous specific proteins (transcription factors) that bind to particular DNA sequences. Without the transcription factors, RNA polymerase II cannot bind to a promoter. However, KNH polymerase II itself is not a transcription factor. The complexity of initiation may derive, in part, from the fact that eukaryotic DNA is in the form of chromatin, which is inaccessible to RNA polymerases. Many RNA polymerase II promoters have the following features  

A sequence, TATAAAT, about 25 bp upstream from the transcription start site, known as the TATA or Hogness box. (Note its similarity to the Pribnow box.) The TATA box probably determines the base that is first transcribed. 

A common sequence in the -75 region, GG(T/C)CAATCT, in which T and C appear with equal frequency at the third position. This sequence is 

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The efficiency and specificity with which an RNA polymerase 11 promoter is recognized depends on short sequences, further away in the 5 direction than the TATA box, that are recognized by more specialized transcription factors. The positions and combinations of these sites vary from promoter to promoter. Most RNA polymerase II promoters contain six or more of these sites and they lie adjacent to the start site of transcription. 

Matis, S., Xu, Y., Shah, M Guan, X., Einstein, J. R., Mural, R. Uberbacher, E. (1996). Detection of RNA polymerase II promoters and polyadenylation sites in human DNA sequence. Comput Chem 20,135-40. 

Bucher, P. (1990). Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol 212,563-78. 

RNA polymerase III promoters differ significantly from RNA polymerase II promoters in that they are located downstream from the transcription start site and within the transcribed segment of the DNA. For example, in the 5S RNA gene of the South African toad Xenopus laevis) the promoter is between 45 and 95 nucleotides downstream from the start point. Thus, the binding sites on RNA polymerase III are reversed with respect to the transcription direction, as compared with RNA polymerase II. That is, RNA polymerase II reaches forward to find the start point, and RNA polymerase III reaches backward. In fact, RNA polymerases can slide in either direction along a DNA template however, they can only synthesize RNA molecules in a 5 3 direction. 

RNA Polymerase II. Promoters for RNA polymerase 0, like prokaryotic promoters, include a set of conserved-sequence elements that define the start site and recruit the polymerase. However, the promoter can contain any combination of a number of possible elements. Unique to eukaryotes, tliey also include enhancer elements that can be very distant (more than 1 kb) from the start site (p. 838). 

When the virus was used to infect a known, fully permissive cell line from Spodoptera frugiperdaf both genes were expressed. CAT activity was detected early in the infection at about six hours, a not surprising result since the RSV LTR contains an RNA polymerase II promoter and this enzymatic activity, pre-existing in the cell, should be amongst the first to act on the viral chromosome. Late in the infection, at the time that the polyhedrin promoter is known to become active, P-galactosidase activity was detected. 

Donze, D., and Kamakaka, R. T. (2001). RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. EMBO J. 20, 520-531. 

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