Unraveling mechanistic features of RNA polymerase II termination by the 5´-3´ exoribonuclease Rat1

Abstract

The 5-3 exoribonuclease Rat1 promotes termination of RNA polymerase II (RNAPII) on protein-coding genes, but its underlying molecular mechanism is still poorly understood. Using in vitro transcription termination assay, I have found that RNAPII is prone to terminate more effectively by Rat1/Rai1 when its catalytic site is disrupted due to NTP misincorporation, proposing that paused RNAPII often found in vivo near termination sites might adopt similar configuration for Rat1 to trigger termination. Intriguingly, Rat1 does not terminate E. coli RNAP, implying that specific interaction between Rat1 and RNAPII may also contribute to termination. Furthermore, the efficiency of termination increases as the RNA transcript being degraded by Rat1 gets longer. It suggests that Rat1 may generate a driving force for dissociating RNAPII from the template while degrading the nascent transcripts to catch up the polymerase. These results indicate that multiple mechanistic features contribute to Rat1-mediated termination of RNAPII.