The RNA polymerases promoters

RNA polymerase I promoter region

RNA polymerase III core promoter

RNA polymerase II promoter

Promoters used by RNA polymerase II have different structures depending upon the particular combination of transcription factors that are required to build a functional transcriptional complex at each promoter. Nevertheless, these different structures can be viewed as a combination of a relatively limited number of specific sequence elements. Some of the common elements that have been described in class II eukaryotic promoters are the following:

The TATA Box located approximately 30 bp upstream of the startpoint of transcription is found in many promoters. The consenus sequence of this element is TATAAAA (so it resembles the TATAAT sequence of the prokaryotic -10 region but please do not mix them up).

 The TATA box appears to be more important for selecting the startpoint of transcription (i.e. positioning the enzyme) than for defining the promoter.

RNA polymerase II promoter

The transcriptional complex

When it was first purified and characterized, it was found that RNA polymerase II can transcribe mRNA in vitro as long as a suitable template -such as a nicked dsDNA or ssDNA -- is provided . The fact that the enzyme could not initiate transcription correctly on a dsDNA template indicated that RNA polymerase II could not function alone in the cell nucleus and a search was begun for additional transcription factors. At least six general (or basal) transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH) have been characterized. In the presence of these transcription factors, the enzyme is able to initiate transcription at promoters correctly. It has been suggested that the combination of RNA polymerase II, transcription factors, and regulatory response complexes such as the mediator, is the eukaryotic equivalent of a holoenzyme in prokaryotic cells.

The RNA polymerase II transcriptional complex

The basic process is likely to include the following steps:

1- TFIID recognizes and binds to the TATA box. TFIID consists of TATA box binding protein - TBP and ~10 TBP associated factors - TAFs. TBP is a 180 amino acid protein that consists of two very similar 66 amino acid domains separated by a short basic region.

TFIID is a positional factor - it targets RNA polymerase to the promoter. In the case of class II transcriptional units, however, TBP binds directly to DNA.

2- TFIIA binds and stabilizes TFIID binding.

3- The RNA polymerase II holoenzyme assembles - possibly in a stepwise manner to form a preinitiation complex.

The holoenzyme consists of the RNA polymerase II complex, the regulatory complexes and the following transcription factors: 1- TFIIB is a single polypeptide. It can bind both upstream and downstream of the TATA box. It recruits TFIIF-RNAPII to the complex. It may interact directly with RNAP II.

2- TFIIE is a complex of two subunits. It recruits TFIIH to the complex thereby priming the initiation complex for promoter clearance and elongation.
3- TFIIF also has two subunits - RAP38 & RAP74. The latter has a helicase activity and may therefore be involved in melting the DNA at the promoter to expose the template strand. 4- TFIIH is a complex of 9 subunits. One of the subunits has a kinase activity that carries out the phosphorylation that is required for promoter clearance

Transcription initiation by RNA polymerase II

Expression of mRNA in Eukaryotic cells requires transcription, modification, processing, nucleo-cytoplasmic transport and translation

The structure and formation of the 5 RNA cap

Polyadenylation and termination