The Mechanisms of Transcription Termination by RNA Polymerase II

Abstract

RNA polymerase II (Pol II) catalyses the transcription of many RNA classes including protein-coding, small nuclear RNA (snRNAs) and some non-coding RNA classes within eukaryotes. Its journey is ended by the cessation of transcription and the dissolution of the DNA-bound complex in a process known as transcriptional termination. Given the diverse array of transcript classes, several termination mechanisms can induce Pol II termination. One of the most studied is polyadenylation signal (PAS)-dependent termination and occurs at the ends of most protein-coding as well as some other transcript classes. Two long-standing models have been used to explain the role of the PAS in termination and their relevance has been a topic of much debate. The allosteric model suggests Pol II undergoes conformational changes after the PAS to instigate termination, while the torpedo model suggests degradation of the downstream RNA product of PAS-cleavage is important to instigate termination. Here, rapid depletion cell lines are employed to describe the widespread dependence of protein-coding transcript termination on the XRN2 torpedo and the CPSF73 PAS-cleaving endonuclease. CPSF73 depletion leads to profound “run-away” transcription, whereas XRN2 depletion results in a more limited read-through. XRN2 targets Pol II complexes that have undergone slowing or pausing in a protein phosphatase 1 (PP1)-mediated process occurring downstream of the PAS. Additionally, XRN2 can degrade RNA and cause torpedo termination from some other PAS-independent cleavage events. However, this is not a universal process with XRN2 dispensable at snRNA and histone transcripts. Together these results suggest a unified allosteric/torpedo mechanism at protein-coding transcripts, where PAS cleavage precedes a PP1-dependent slowing of Pol II. This facilitates the degradation of downstream RNA by XRN2 and thereby instigates transcriptional termination.