RNA polymerase I

RNA polymerase I (also called Pol I) is, in eukaryotes, the only enzyme that transcribes ribosomal RNA (excluding 5S rRNA, which is synthesized by RNA Polymerase III), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell.

Pol I consists of 8-14 protein subunits (polypeptides). All 12 subunits have identical or related counterparts in Pol II and Pol III. rDNA transcription is confined to the nucleolus where several hundreds of copies of rRNA genes are present, arranged as tandem head-to-tail repeats. Pol I transcribes one large transcript, encoding an rDNA gene over and over again. This gene encodes the 18S, the 5.8S, and the 28S RNA molecules of the ribosome in eukaryotes. The transcripts are cleaved by snoRNA. The 5S ribosomal RNA is transcribed by Pol III. Because of the simplicity of Pol I transcription, it is the fastest-acting polymerase.

Regulation of rRNA transcription
The rate of cell growth is directly dependent on the rate of protein synthesis, which, itself, is intricately linked to ribosome synthesis and rRNA transcription. Thus, intracellular signals must coordinate the synthesis of rRNA with that of other components of protein translation. Two specific mechanisms have been identified, ensuring proper control of rRNA synthesis and Pol I-mediated transcription.

Given the large number of rDNA genes (several hundreds) available for transcription, the first mechanism involves adjustments in the number of genes being transcribed at a specific time. In mammalian cells, the number of active rDNA genes varies between cell types and level of differentiation. In general, as a cell become more differentiated, it requires less growth and, therefore, will have a decrease in rRNA synthesis and a decrease in rDNA genes being transcribed. When rRNA synthesis is stimulated, SL1 (selectivity factor 1) will bind to the promoters of rDNA genes that were previously silent, and recruit a pre-initiation complex to which Pol I will bind and start transcription of rRNA.

Changes in rRNA transcription can also occur via changes in the rate of transcription. While the exact mechanism through which Pol I increases its rate of transcription is yet unknown, evidence has shown that rRNA synthesis can increase or decrease without changes in the number of actively transcribed rDNA.

Pol I transcription cycle
In the process of transcription (by any polymerase), there are three main stages:
 * 1) Initiation: the construction of the RNA polymerase complex on the gene's promoter with the help of transcription factors
 * 2) Elongation: the actual transcription of the majority of the gene into a corresponding RNA sequence
 * 3) Termination: the cessation of RNA transcription and the disassembly of the RNA polymerase complex.

Initiation
Initiation: the construction of the polymerase complex on the promoter. Pol I requires no TATA box in the promoter, instead relying on a UCS (Upstream Control Sequence).


 * 1) UBF (Upstream Binding Factor) binds the UCS.
 * 2) UCS recruits and binds a protein complex incorporating TBP (TATA Binding Protein) and three TAFs (TBP Associated Factors) called SL1 or TIF-IB. The TBP is forced to bind non-sequence specifically.
 * 3) Rrn3/TIF-IA gets phosphorylated and binds Pol I
 * 4) Pol I binds to the UBF/SL1 complex via Rrn3/TIF-IA, and transcription starts.

Elongation
As Pol I escapes and clears the promoter, UBF and SL1 remain-promoter bound, ready to recruit another Pol I. Indeed, each active rDNA gene can be transcribed multiple times simultaneously, as opposed to Pol II-transcribed genes, which associate with only one complex at a time. While elongation proceeds unimpeded in vitro, it is unclear at this point whether this process happens in a cell, given the presence of nucleosomes. Pol I does seem to transcribe through nucleosomes, either bypassing or disrupting them, perhaps assisted by chromatin-remodeling activities. In addition, UBF might also act as positive feedback, enhancing Pol I elongation through an anti-repressor function. An additional factor, TIF-IC, can also stimulate the overall rate of transcription and suppress pausing of Pol I. As Pol I proceeds along the rDNA, supercoils form both ahead and behind the complex. These are unwound by topoisomerase I or II at regular interval, similar to what is seen in Pol II-mediated transcription.

Elongation is likely to be interrupted at sites of DNA damage. Transcription-coupled repair occurs similarly to Pol II-transcribed genes and require the presence of several DNA repair proteins, such as TFIIH, CSB, and XPG.

Termination
In higher eukaryotes, TTF-I binds and bends the termination site at the 3' end of the transcribed region. This will force Pol I to pause. TTF-I, with the help of transcript-release factor PTRF and a T-rich region, will induce Pol I into terminating transcription and dissociating from the DNA and the new transcript. Evidence suggests that termination might be rate-limiting in cases of high rRNA production. TTF-I and PTRF will then indirectly stimulate the reinitiation of transcription by Pol I at the same rDNA gene. In organisms such as budding yeast the process seems to be much more complicated and is still not completely elucidated.