RNA polymerase III
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.
In the process of transcription (by any polymerase) there are three main stages:
- Initiation, requiring construction of the RNA polymerase complex on the gene's promoter.
- Elongation, the synthesis of the RNA transcript.
- Termination, the finishing of RNA transcription and disassembly of the RNA polymerase complex.
Initiation: the construction of the polymerase complex on the promoter. Pol III is unusual (compared to Pol II) by requiring no control sequences upstream of the gene, instead normally relying on internal control sequences - sequences within the transcribed section of the gene (although upstream sequences are occasionally seen, e.g. U6 snRNA gene has an upstream TATA box as seen in Pol II Promoters).
Typical stages in 5S rRNA (also termed class I) gene initiation:
- TFIIIA (Transcription Factor for polymerase III A) binds to the intragenic (lying within the transcribed DNA sequence) 5S rRNA control sequence, the C Block (also termed box C).
- 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.
Typical stages in a tRNA (also termed class II) gene initiation:
- TFIIIC (Transcription Factor for polymerase III C) binds to two intragenic (lying within the transcribed DNA sequence) control sequences, the A and B Blocks (also termed box A and box B).
- 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 (Transcription Factor for polymerase III B), consists of three subunits: TBP (TATA Binding Protein), the Pol II transcription factor TFIIB-related protein, BRF1 (or Brf2 for transcription of a subset of Pol III-transcribed genes in vertebrates) and BDP1.
- TFIIB is the transcription factor that assembles Pol III at the start site of transcription. Once TFIIB is bound to DNA, TFIIIC is no longer required. TFIIB also plays an essential role in promoter opening.
TFIIB remains bound to DNA following initiation of transcription by Pol III (unlike bacterial σ factors and most of the basal transcription factors for Pol II transcription). This leads to a high rate of transcriptional reinitiation of Pol III-transcribed genes.
Typical stages in a U6 snRNA (also termed class III) gene initiation (documented in vertebrates only):
- SNAPc (SNRNA Activating Protein complex) (also termed PBP and PTF) binds to the PSE (Proximal Sequence Element) 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 (Distal Sequence Element) 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 TFIIB 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 TFIIB for U6 snRNA transcription contains a smaller Brf1 paralogue, Brf2.
- TFIIB is the transcription factor that assembles Pol III at the start site of transcription. Sequence conservation predicts that TFIIB containing Brf2 also plays a role in promoter opening.
The types of RNAs transcribed from RNA polymerase III includes:
- Transfer RNAs
- 5S ribosomal RNA
- U6 spliceosomal RNA
- RNase P and RNase MRP RNA
- 7SL RNA (the RNA component of the signal recognition particle)
- Vault RNAs
- Y RNA
- SINEs (short interspersed repetitive elements)
- 7SK RNA
- Several microRNAs
- Several small nucleolar RNAs
- Several gene regulatory antisense RNAs
- Vannini, A.; Ringel, R.; Kusser, A. G.; Berninghausen, O.; Kassavetis, G. A.; Cramer, P. (2010). "Molecular Basis of RNA Polymerase III Transcription Repression by Maf1". Cell. 143 (1): 59–70. doi:10.1016/j.cell.2010.09.002. PMID 20887893.
- Oettel S, Kober I, Seifart KH (October 1998). "The activity binding to the termination region of several pol III genes represents a separate entity and is distinct from a novel component enhancing U6 snRNA transcription.". Nucleic Acids Research. 26 (19): 4324–31. doi:10.1093/nar/26.19.4324. PMC . PMID 9742231.
- Ishiguro A, Kassavetis GA, Geiduschek EP (May 2002). "Essential roles of Bdp1, a subunit of RNA polymerase III initiation factor TFIIIB, in transcription and tRNA processing.". Molecular and cellular biology. 22 (10): 3264–75. doi:10.1128/MCB.22.10.3264-3275.2002. PMC . PMID 11971960.
- Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A (December 2007). "The expanding RNA polymerase III transcriptome". Trends Genet. 23 (12): 614–22. doi:10.1016/j.tig.2007.09.001. PMID 17977614.
- Pagano A, Castelnuovo M, Tortelli F, Ferrari R, Dieci G, Cancedda R (February 2007). "New small nuclear RNA gene-like transcriptional units as sources of regulatory transcripts". PLoS Genet. 3 (2): e1. doi:10.1371/journal.pgen.0030001. PMC . PMID 17274687.