In eukaryote cells, RNA polymerase IIItranscribesDNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs. The genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose expression is required in all cell types and most environmental conditions. Therefore, the regulation of Pol III transcription is primarily tied to the regulation of cell growth and the cell cycle, thus requiring fewer regulatory proteins than RNA polymerase II. Under stress conditions however, the protein Maf1 represses Pol III activity. Rapamycin is another Pol III inhibitor via its direct target TOR.
Transcription
The process of transcription involves three main stages:
Initiation, requiring construction of the RNA polymerase complex on the gene's promoter
Termination, the finishing of RNA transcription and disassembly of the RNA polymerase complex
Initiation
Initiation: the construction of the polymerase complex on the promoter. Pol III is unusual by requiring no control sequences upstream of the gene, instead normally relying on internal control sequences - sequences within the transcribed section of the gene. There are three classes of Pol III initiation, corresponding to 5S rRNA, tRNA, and U6 snRNA initiation. In all cases, the process starts with transcription factors binding to control sequences, and ends with TFIIIB being recruited to the complex and assembling Pol III. TFIIIB consists of three subunits: TATA binding protein, a TFIIB-related factor, and a B-double-prime unit. The overall architecture bears similarities to that of Pol II.
Class I
Typical stages in 5S rRNA gene initiation:
TFIIIA binds to the intragenic 5S rRNA control sequence, the C Block.
TFIIIA serves as a platform that replaces the A and B Blocks for positioning TFIIIC in an orientation with respect to the start site of transcription that is equivalent to what is observed for tRNA genes.
Once TFIIIC is bound to the TFIIIA-DNA complex, the assembly of TFIIIB proceeds as described for tRNA transcription.
Class II
Typical stages in a tRNA gene initiation:
TFIIIC binds to two intragenic control sequences, the A and B Blocks.
TFIIIC acts as an assembly factor that positions TFIIIB to bind to DNA at a site centered approximately 26 base pairs upstream of the start site of transcription.
TFIIIB is the transcription factor that assembles Pol III at the start site of transcription. Once TFIIIB is bound to DNA, TFIIIC is no longer required. TFIIIB also plays an essential role in promoter opening.
Class III
Typical stages in a U6 snRNA gene initiation :
SNAPc binds to the PSE centered approximately 55 base pairs upstream of the start site of transcription. This assembly is greatly stimulated by the Pol II transcription factors Oct1 and STAF that bind to an enhancer-like DSE at least 200 base pairs upstream of the start site of transcription. These factors and promoter elements are shared between Pol II and Pol III transcription of snRNA genes.
SNAPc acts to assemble TFIIIB at a TATA box centered 26 base pairs upstream of the start site of transcription. It is the presence of a TATA box that specifies that the snRNA gene is transcribed by Pol III rather than Pol II.
The TFIIIB for U6 snRNA transcription contains a smaller Brf1 paralogue, Brf2.
TFIIIB is the transcription factor that assembles Pol III at the start site of transcription. Sequence conservation predicts that TFIIIB containing Brf2 also plays a role in promoter opening.
Elongation
TFIIIB remains bound to DNA following initiation of transcription by Pol III. This leads to a high rate of transcriptional reinitiation of Pol III-transcribed genes.
Termination
Polymerase III terminates transcription at small polyTs stretch. In eukaryotes, a hairpin loop is not required, as it is in prokaryotes.
Transcribed RNAs
The types of RNAs transcribed from RNA polymerase III include:
