Transcription termination by the eukaryotic RNA polymerase III

Abstract

RNA polymerase (pol) III transcribes a multitude of tRNA and 5S rRNA genes as well as other small RNA genes distributed through the genome. By being sequence-specific, precise and efficient, transcription termination by pol III not only defines the 3′ end of the nascent RNA which directs subsequent association with the stabilizing La protein, it also prevents transcription into downstream DNA and promotes efficient recycling. Each of the RNA polymerases appears to have evolved unique mechanisms to initiate the process of termination in response to different types of termination signals. However, in eukaryotes much less is known about the final stage of termination, destabilization of the elongation complex with release of the RNA and DNA from the polymerase active center. By comparison to pols I & II, pol III exhibits the most direct coupling of the initial and final stages of termination, both of which occur at a short oligo(dT) tract on the non-template strand (dA on the template) of the DNA. While pol III termination is autonomous involving the core subunits C2 and probably C1, it also involves subunits C11, C37 and C53, which act on the pol III catalytic center and exhibit homology to the pol II elongation factor TFIIS, and TFIIFα/β respectively. Here we compile knowledge of pol III termination and associate mutations that affect this process with structural elements of the polymerase that illustrate the importance of C53/37 both at its docking site on the pol III lobe and in the active center. The models suggest that some of these features may apply to the other eukaryotic pols.

RNA polymerase I structure and transcription regulation

“…16). The composite active site of Pol I and III enables efficient proofreading 9,17 and termination 18,19 .…”

Comparative overview of RNA polymerase II and III transcription cycles, with focus on RNA polymerase III termination and reinitiation

“…70,75 Other functions of these S-like RNA cleavage factors include removal of misincorporated nucleotides and rescue of RNA polymerases that are inactivated by stalling or backtracking. 76 RNA polymerases tend to backtrack when faced with transcription roadblocks or when the RNA-DNA hybrid that forms in the transcription bubble is of very weak thermo stability, such as when formed of oligo(rU:dA). 77 During backtracking, the 3′ end of the nascent RNA in the RNA:DNA hybrid is unzipped and its 3′ end can fray and protrude from a conserved tunnel feature known as the secondary channel that connects the catalytic center to outside of the polymerase.…”

“…Indeed, even the simplest of these, bacterial RNAP, requires a bipartite termination signal in the DNA and a two-component mechanism by the polymerase for intrinsic (factor-independent) termination. 76 As part of the adaptation by RNAP III for short gene transcripts, the benefit of a facile termination mechanism may offset the relatively low risk of premature truncation.…”

“…76 For RNAP I and RNAP II, as well as for bacterial and archaeal RNAPs (all of which synthesize relatively long transcripts), the stability of elongation complexes (ECs) should be very important because of the risk of wasteful production of truncated functionless RNAs (or worse, dominant negative transcripts). Accordingly, the programmed dismantling of these elongation complexes at termination may be expected to be multipartite and intricate.…”

tsRNA signatures in cancer

“…Recently, a class of small ncRNAs was reported to derive from tRNA precursor or mature sequences, and their connection with cancer is currently under investigation (4). In eukaryotic cells, tRNAs are transcribed by RNA polymerase III, with transcription terminating after a stretch of four or more Ts located 10-60 nt downstream of the 3′ end of the tRNA mature sequence (5,6). Pre-tRNAs and mature tRNAs undergo extensive modifications before and after exportation to the cytoplasm (7) resulting in the production of three types of tRNA-derived ncRNAs: tRNA-derived small RNAs (tsRNAs) (4), tRNA halves (tiRNAs) (8), and tRNA-derived fragments (tRFs or tDRs) (9,10).…”