Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation

Vos, Seychelle M.; Farnung, Lucas; Linden, Andreas; Urlaub, Henning; Cramer, Patrick

doi:10.1038/s41594-020-0437-1

Cited by 160Genomics and Chromatin DynamicsNuclear Structure and FunctionChromatin Remodeling and Cancer

Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation

Vos, Seychelle M., Farnung, Lucas, Linden, Andreas, Urlaub, Henning, Cramer, Patrick·2020·Nature Structural & Molecular Biology

DOI 10.1038/s41594-020-0437-1

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Abstract

Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation factors DSIF, PAF1 complex (PAF) and SPT6. Here we report the cryo-EM structure of the complete EC* that contains RTF1, a dissociable PAF subunit critical for chromatin transcription. The RTF1 Plus3 domain associates with Pol II subunit RPB12 and the phosphorylated C-terminal region of DSIF subunit SPT5. RTF1 also forms four α-helices that extend from the Plus3 domain along the Pol II protrusion and RPB10 to the polymerase funnel. The C-terminal 'fastener' helix retains PAF and is followed by a 'latch' that reaches the end of the bridge helix, a flexible element of the Pol II active site. RTF1 strongly stimulates Pol II elongation, and this requires the latch, possibly suggesting that RTF1 activates transcription allosterically by influencing Pol II translocation.

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Rtf1 increases RNA Pol II speed in in vitro transcription assays.
“On the other hand, consistent with a role of the Paf1C complex in RNA Pol II speed regulation, recent data show that the dissociable Paf1C subunit Rtf1 increases RNA Pol II speed in in vitro transcription assays (Vos et al, 2020).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Vos et al, 2020
Recruitment of the PAF complex via a flexible AFF4 scaffold ensures transcript elongation, providing the structural basis for the transition from pausing to active elongation.
“During this process, the recruitment of the PAF complex via a flexible AFF4 scaffold ensures transcript elongation, providing the structural basis for the transition from pausing to active elongation (Feinberg et al. 1991, Chou et al. 2013, Vos et al. 2020).”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Vos et al. 2020

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Deng, P., Zhou, Y., Jiang, J., Li, H., Tian, W., Cao, Y., Qin, Y. L., Kim, J., Roeder, R. G., Patel, D. J., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1812256115 · Cited by 23 · see citing works
Structure of mammalian RNA polymerase II elongation complex inhibited by Alpha-amanitin
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RNA polymerase II speed: a key player in controlling and adapting transcriptome composition
Muniz, L., Nicolas, E., & Trouche, D. (2021) · The EMBO Journal · doi:10.15252/embj.2020105740 · Cited by 203 · see citing works
“On the other hand, consistent with a role of the Paf1C complex in RNA Pol II speed regulation, recent data show that the dissociable Paf1C subunit Rtf1 increases RNA Pol II speed in in vitro transcription assays (Vos et al , 2020).”
The Paf1 complex is required for RNA polymerase II removal in response to DNA damage
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Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication
Jehad, M. A., Ali, L. M., Pillai, V. N., Prabhu, S. G., Mustafa, F., & Rizvi, T. A. (2026) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaf066 · Cited by 5 · see citing works
“During this process, the recruitment of the PAF complex via a flexible AFF4 scaffold ensures transcript elongation, providing the structural basis for the transition from pausing to active elongation (Feinberg et al. 1991 , Chou et al. 2013 , Vos et al. 2020 ).”

Ctk1 promotes dissociation of basal transcription factors from elongating RNA polymerase II
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TFIIH Phosphorylation of the Pol II CTD Stimulates Mediator Dissociation from the Preinitiation Complex and Promoter Escape
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RNA Polymerase II Holoenzyme and Transcription Factors
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Mechanism of assembly of the RNA polymerase II preinitiation complex. Evidence for a functional interaction between the carboxyl-terminal domain of the largest subunit of RNA polymerase II and a high molecular mass form of the TATA factor.
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Sub1 associates with Spt5 and influences RNA polymerase II transcription elongation rate
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Authors: Vos, S. M., Farnung, L., Linden, A., Urlaub, H., & Cramer, P.
Affiliations: Max Planck Institute for Biophysical Chemistry (DE)
Universitätsmedizin Göttingen (DE)
Corresponding author: Cramer, Patrick
ORCID: Vos, Seychelle M.
Farnung, Lucas
Linden, Andreas
Urlaub, Henning
Cramer, Patrick
Venue: Nature Structural & Molecular Biology
Publisher: Springer Science and Business Media LLC
Published: 2020-06-15
Volume: 27
Issue: 7
Pages: 668-677
ISSN: 1545-9985 (ISSN-L)
1545-9993
DOI: 10.1038/s41594-020-0437-1
OpenAlex: W3035713655
Cited by: 160
References: 80
Citations by year: 2026: 18 · 2025: 27 · 2024: 30 · 2023: 31 · 2022: 25 · 2021: 23 · 2020: 6
FWCI: 6.89
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature Structural & Molecular Biology (publishedVersion)
PubMed (publishedVersion)
MPG.PuRe (Max Planck Society) (submittedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords: RNA polymerase II, transcription elongation, Rtf1, Paf1 complex, DSIF, Spt6, allosteric activation, bridge helix, chromatin transcription, cryo-EM structure
MeSH terms: Allosteric Regulation, Humans, Models, Molecular, Nuclear Proteins, Protein Binding, Protein Conformation, RNA Polymerase II, Transcription Factors, Transcription, Genetic, Cryoelectron Microscopy, Transcriptional Elongation Factors, Multiprotein Complexes

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Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation

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