The nuclei of eukaryotic cells contain three RNA polymerases (designated I, II and III). These enzymes catalyze the formation of the phosphodiester bond that links nucleotides together to form a linear chain. Transcription by RNA polymerase III produces small, stable RNAs including tRNAs, the 5S rRNA associated with the large ribosomal subunit, one of the snRNAd required for pre-mRNA splicing, and the 7S RNA associated with the signal recognition particle involved in secretion of proteins and insertion of membrane spanning proteins into cellular membranes. The functions of many other small RNAs produced by RNA polymerase III are as yet undiscovered.
Recognition of promoters by RNA polymerase III illustrates strikingly the relative roles of transcription factors and the polymerase enzyme. The promoters for 5S and tRNA genes are internal; they lie downstream of the start point. In both cases, the individual elements that are necessary for promoter function consist exclusively of sequences recognized by transcription factors which in turn direct the binding of RNA polymerase III. The transcription control regions of tRNA genes lie entirely within the transcribed sequence. These DNA sequences encode the most highly conserved portions of eukaryotic tRNAs, the D-loop and the T*PCG loop which are referred to as the A-Box and B-Box. They serve two distinct purposes: (1) They encode essential regions of tRNA molecules required for protein synthesis, and (2) They bind proteins necessary for transcription initiation by RNA polymerase III.
The DNA binding factors required for RNA polymerase III to initiate transcription have been best characterized in Saccharomyces cerevisiae. Assembly of the initiation complex on tRNA genes begins by binding of TFIIIC to the A-Box and B-Box in the promoter. TFIIIB then binds ~50bp upstream of the A-Box. TFIIIB can bind to many different sequences at this position, indicating that specific binding is via its interaction with TFIIIC rather than by sequence specific interactions with DNA. TFIIIC is composed of six polypeptides with a total molecular weight of ~600kDa. TFIIIB is made up of three subunits: TATA-binding protein (TBP), TFIIB-related factor (BRF) and a 90kDa polypeptide called 'B'. Once TFIIIB has bound, RNA polymerase III can bind and initiate transcription and TFIIIC can be removed without affecting initiation by RNA polymerase III. Thus, TFIIIC serves as an assembly factor while TFIIIB functions as a 'positioning factor', responsible for localizing RNA polymerase III correctly.
In addition to TFIIIC and TFIIIB, transcription of 5S-rRNA genes requires a third initiation factor called TFIIIA. TFIIIA is a member of zinc finger proteins. Binding of this factor (a monomer) to the 5S-rRNA gene begins assembly of the initiation complex. The binding site for TFIIIA, called the C-Box is located 81-99bp downstream from the start site. It is an internal control region like the A and B-Boxes of tRNA genes. TFIIIA binding is followed by the binding of TFIIIC and TFIIIC, similar to the tRNA gene. Once TFIIIB has bound, RNA polymerase III binds and initiates transcription.