Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a “Sitting Duck Torpedo” Mechanism
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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.
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Transcription of the poly(A) site induces allosteric changes in the elongation complex mediated by dephosphorylation of Spt5 by PP1, which slow down elongation by at least two- to threefold.
“In addition, transcription of the poly(A) site induces allosteric changes in the elongation complex (Logan et al, 1987) mediated by dephosphorylation of Spt5 by the PP1 phosphatase, which slow down elongation by at least two‐ to threefold (Cortazar et al, 2019).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Cortazar et al, 2019
The Discussion reports that median elongation rates fall from 2–3 kb/min in gene bodies to 0.1–0.9 kb/min downstream of poly(A) sites. It also proposes that poly(A)-dependent Spt5 dephosphorylation by PNUTS-PP1 helps mediate the slowdown, but describes this mechanism as suggested and potentially indirect, rather than established as the sole cause. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIn mammalian cells most studies only consider very long genes to accurately decipher an elongation speed.
“Indeed, in mammalian cells most studies only consider very long genes to accurately decipher an elongation speed (Saponaro et al, 2014; Cortazar et al, 2019; Gregersen et al, 2019; Hou et al, 2019; Sheridan et al, 2019; Fan et al, 2020).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Cortazar et al, 2019
The STAR Methods (Calculation of elongation rates; page not provided) restrict gene-body elongation-rate analyses to non-overlapping genes longer than 60 kb, supporting this paper as an example of using long genes for that measurement. The same section uses genes shorter than 20 kb to measure rates in termination zones, and the paper does not establish that most mammalian-cell studies consider only very long genes. (LLM, conf=0.85)
Experimental — accuracy not yet measuredReduction of elongation speed at the poly(A) site facilitates catch-up of RNA Pol II by the Xrn2 exonuclease, which dislodges RNA Pol II from the DNA template leading to transcription termination.
“This reduction of elongation speed facilitates the catch‐up of RNA Pol II by the Xrn2 exonuclease, which dislodges RNA Pol II from the DNA template leading to transcription termination (Cortazar et al, 2019; Eaton et al, 2020).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Cortazar et al, 2019
PP1 phosphatase together with PNUTS can dephosphorylate Spt5, which slows down RNA Pol II transcription in human cells.
“Nevertheless, consistent with a role of Spt5 in the regulation of RNA Pol II speed, the PP1 phosphatase together with its nuclear targeting subunit (PNUTS) can dephosphorylate Spt5, which slows down RNA Pol II transcription in human cells (Cortazar et al, 2019).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Cortazar et al, 2019
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RNA polymerase II speed: a key player in controlling and adapting transcriptome composition
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“In addition, transcription of the poly(A) site induces allosteric changes in the elongation complex (Logan et al , 1987) mediated by dephosphorylation of Spt5 by the PP1 phosphatase, which slow down elongation by at least two-to threefold (Cortazar et al , 2019).”
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Lee, Y., Biasini, A., Tipping, C., Hong, S. H., & Zamore, P. D. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116329 · Cited by 6 · see citing works
- Authors
- Cortazar, M. A., Sheridan, R. M., Erickson, B., Fong, N., Glover-Cutter, K., Brannan, K., & Bentley, D. L.
- Affiliations
- University of Colorado Anschutz (US)
- Corresponding author
- Bentley, David L.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2019-12
- Volume
- 76
- Issue
- 6
- Pages
- 896-908.e4
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC6927536
- OpenAlex
- W2982494755
- Cited by
- 227
- References
- 78
- Citations by year
- 2026: 24 · 2025: 27 · 2024: 52 · 2023: 41 · 2022: 20 · 2021: 39 · 2020: 21 · 2019: 2
- FWCI
- 6.79
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- transcription termination, NusG
- MeSH terms
- Binding Sites, DNA-Binding Proteins, Exoribonucleases, Humans, Kinetics, Nuclear Proteins, Phosphorylation, Poly A, Protein Binding, Protein Processing, Post-Translational, RNA Polymerase II, RNA, Messenger, Signal Transduction, RNA-Binding Proteins, Transcriptional Elongation Factors, Protein Phosphatase 1, HEK293 Cells, Transcription Termination, Genetic
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