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RNA polymerase II
RNA polymerase II (also called RNAP II and Pol II) is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to its promoters and begin transcription.
Additional recommended knowledge
Stages of transcription
In the process of transcription (by any polymerase) there are three main stages:
Due to the range of genes Pol II transcribes this is the polymerase that experiences greatest regulation, by a range of factors, at each stage of transcription. It is also one of the most complex in terms of polymerase cofactors involved.
Preinitiation complex (PIC): the construction of the polymerase complex on the promoter. The TATA box is one well-studied example of a promoter element. It is conserved in many (though not all) model eukaryotes and is found in a fraction of the promoters in these organisms. The sequence TATA is located at approximately 25 nucleotides upstream of the Transcription Start Point (TSP). In addition, there are also some weakly conserved features including the B-Recognition Element (BRE), approximately 5 nucleotides upstream of the TATA box.
Order in which the GTFs attach
The following is the order in which the GTFs (general transcription factors) attach:
†Occasionally there is no TATA box at the promoter. In this case a TAF will bind sequence specifically, and force the TBP to bind non sequence specifically. TAFs are highly variable, and add a level of control to the initiation.
Initiation is regulated by many mechanisms. These can be separated into two main categories:
Regulation by Protein interference
Protein interference is the process where some signaling protein interacts, either with the promoter or some stage of the partially constructed complex, to prevent further construction of the polymerase complex, so preventing initiation. This is generally a very rapid response and is used for fine level, individual gene control and for 'cascade' processes for a group of genes useful under a specific conditions (for example DNA repair genes or heat shock genes)
Chromatin structure inhibition is the process where the promoter is hidden by chromatin structure. Chromatin structure is controlled by post-translational modification of the histones involved and leads to gross levels of high or low transcription levels. See: chromatin, histone and nucleosome. For a detailed treatment of a single example see: RNA polymerase control by chromatin structure.
These methods of control can be combined in a modular method, allowing very high specificity in transcription initiation control.
Regulation by Phosphorylation
The largest subunit of Pol II (Rpb1) has a domain at its C-terminus that is called the CTD (C-terminal domain). This is the target of kinases and phosphatases. The phosphorylation of the CTD is an important regulation mechanism, as this allows attraction and rejection of factors that have a function in the transcription process. The CTD can be considered as a platform for transcription factors.
The CTD consists of repetitions of an amino acid motif, YSPTSPS, of which Serines and Threonines can be phosphorylated. The number of these repeats varies; the mammalian protein contains 52, while the yeast protein contains 26. Site-directed-mutagenesis of the yeast protein has found at least 10 repeats are needed for viability. There are many different combinations of phosphorylations possible on these repeats and these can change rapidly during transcription. The regulation of these phosphorylations and the consequences for the association of transcription factors plays a major role in the regulation of transcription.
During the transcription cycle, the CTD of the large subunit of RNAP II is reversibly phosphorylated. RNAP II containing unphosphorylated CTD is recruited to the promoter, whereas the hyperphosphorylated CTD form is involved in active transcription. Phosphorylation occurs at two sites within the heptapeptide repeat, at Serine 5 and Serine 2. Serine 5 phosphorylation is confined to promoter regions and is necessary for the initiation of transcription, whereas Serine 2 phosphorylation is important for mRNA elongation and 3'-end processing.
The process of elongation is the synthesis of a copy of the DNA into messenger RNA. RNA Pol II matches complementary RNA nucleotides to the template DNA by Watson-Crick base pairing. These RNA nucleotides are ligated and this results in a strand of messenger RNA.
RNA Pol II elongation promoters can be summarised in 3 classes:
As for initiation, protein interference, seen as the "drug/sequence-dependent arrest affected factors" and "RNA Pol II catalysis improving factors" provide a very rapid response and is used for fine level individual gene control. Elongation downregulation is also possible, in this case usually by blocking polymerase progress or by deactivating the polymerase.
Chromatin structure oriented factors are more complex than for initiation control. Often the chromating altering factor becomes bound to the polymerase complex, altering the histones as they are encountered and providing a semi-permanent 'memory' of previous promotion and transcription. For detailed treatment of an example see: RNA polymerase control by chromatin structure.
Termination is the process of breaking up of the polymerase complex and ending of the RNA strand. In eukaryotes using RNA Pol II this termination is very variable (up to 2000 bases), relying on post transcriptional modification. See: Messenger RNA and Polyadenylation.
Little regulation occurs at termination, although it has been proposed newly transcribed RNA is held in place if proper termination is inhibited, allowing very fast expression of genes given a stimulus. This has not been demonstrated in eukaryotes as of yet.
|This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "RNA_polymerase_II". A list of authors is available in Wikipedia.|