Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a “Sitting Duck Torpedo” Mechanism

Michael A. Cortazar, Ryan M. Sheridan, Benjamin Erickson, Nova Fong, Kira Glover-Cutter, Kristopher Brannan, David L. Bentley

Research output: Contribution to journalArticlepeer-review


Control of transcription speed, which influences many co-transcriptional processes, is poorly understood. We report that PNUTS-PP1 phosphatase is a negative regulator of RNA polymerase II (Pol II) elongation rate. The PNUTS W401A mutation, which disrupts PP1 binding, causes genome-wide acceleration of transcription associated with hyper-phosphorylation of the Spt5 elongation factor. Immediately downstream of poly(A) sites, Pol II decelerates from >2 kb/min to <1 kb/min, which correlates with Spt5 dephosphorylation. Pol II deceleration and Spt5 dephosphorylation require poly(A) site recognition and the PNUTS-PP1 complex, which is in turn necessary for transcription termination. These results lead to a model for termination, the “sitting duck torpedo” mechanism, where poly(A) site-dependent deceleration caused by PNUTS-PP1 and Spt5 dephosphorylation is required to convert Pol II into a viable target for the Xrn2 terminator exonuclease. Spt5 and its bacterial homolog NusG therefore have related functions controlling kinetic competition between RNA polymerases and the termination factors that pursue them. RNA polymerase II (Poll II) speed varies widely between genes and within genes. Cortazar et al. show that Pol II speed is limited by the PNUTS-PP1 phosphatase complex that dephosphorylates the elongation factor Spt5, and this mechanism decelerates transcription in termination zones downstream of poly(A) sites. They propose that termination of transcription requires poly(A) site-dependent deceleration of transcription that converts the RNA polymerase into a “sitting duck” for the Xrn2 “torpedo” to track down and dislodge from the DNA template.

Original languageEnglish (US)
Pages (from-to)896-908.e4
JournalMolecular Cell
Issue number6
StatePublished - Dec 19 2019


  • Pol II elongation rate
  • PP1 phosphatase
  • Spt5 phosphorylation
  • transcription termination

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


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