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Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

Author

Listed:
  • Seychelle M. Vos

    (Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology)

  • Lucas Farnung

    (Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology)

  • Marc Boehning

    (Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology)

  • Christoph Wigge

    (Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology)

  • Andreas Linden

    (Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry
    University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group)

  • Henning Urlaub

    (Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry
    University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group)

  • Patrick Cramer

    (Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology)

Abstract

Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we show that formation of an activated Pol II elongation complex in vitro requires the kinase function of the positive transcription elongation factor b (P-TEFb) and the elongation factors PAF1 complex (PAF) and SPT6. The cryo-EM structure of an activated elongation complex of Sus scrofa Pol II and Homo sapiens DSIF, PAF and SPT6 was determined at 3.1 Å resolution and compared to the structure of the paused elongation complex formed by Pol II, DSIF and NELF. PAF displaces NELF from the Pol II funnel for pause release. P-TEFb phosphorylates the Pol II linker to the C-terminal domain. SPT6 binds to the phosphorylated C-terminal-domain linker and opens the RNA clamp formed by DSIF. These results provide the molecular basis for Pol II pause release and elongation activation.

Suggested Citation

  • Seychelle M. Vos & Lucas Farnung & Marc Boehning & Christoph Wigge & Andreas Linden & Henning Urlaub & Patrick Cramer, 2018. "Structure of activated transcription complex Pol II–DSIF–PAF–SPT6," Nature, Nature, vol. 560(7720), pages 607-612, August.
    • Handle: RePEc:nat:nature:v:560:y:2018:i:7720:d:10.1038_s41586-018-0440-4
    DOI: 10.1038/s41586-018-0440-4
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    Cited by:

    1. Wojciech Barczak & Simon M. Carr & Geng Liu & Shonagh Munro & Annalisa Nicastri & Lian Ni Lee & Claire Hutchings & Nicola Ternette & Paul Klenerman & Alexander Kanapin & Anastasia Samsonova & Nicholas, 2023. "Long non-coding RNA-derived peptides are immunogenic and drive a potent anti-tumour response," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Emily G. Kaye & Kavyashree Basavaraju & Geoffrey M. Nelson & Helena D. Zomer & Debarun Roy & Irene Infancy Joseph & Reza Rajabi-Toustani & Huanyu Qiao & Karen Adelman & Prabhakara P. Reddi, 2024. "RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    3. Yan Li & Qianmin Wang & Yanhui Xu & Ze Li, 2024. "Structures of co-transcriptional RNA capping enzymes on paused transcription complex," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    4. Abdallah Gaballa & Anneli Gebhardt-Wolf & Bastian Krenz & Greta Mattavelli & Mara John & Giacomo Cossa & Silvia Andreani & Christina Schülein-Völk & Francisco Montesinos & Raphael Vidal & Carolin Kast, 2024. "PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    5. Lisa-Marie Appel & Vedran Franke & Melania Bruno & Irina Grishkovskaya & Aiste Kasiliauskaite & Tanja Kaufmann & Ursula E. Schoeberl & Martin G. Puchinger & Sebastian Kostrhon & Carmen Ebenwaldner & M, 2021. "PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC," Nature Communications, Nature, vol. 12(1), pages 1-24, December.
    6. Roberto Bandiera & Rebecca E. Wagner & Thiago Britto-Borges & Christoph Dieterich & Sabine Dietmann & Susanne Bornelöv & Michaela Frye, 2021. "RN7SK small nuclear RNA controls bidirectional transcription of highly expressed gene pairs in skin," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    7. Yujuan Liu & Jie Shu & Zhi Zhang & Ning Ding & Jinyuan Liu & Jun Liu & Yuhai Cui & Changhu Wang & Chen Chen, 2024. "A conserved Pol II elongator SPT6L mediates Pol V transcription to regulate RNA-directed DNA methylation in Arabidopsis," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    8. Michael DeBerardine & Gregory T. Booth & Philip P. Versluis & John T. Lis, 2023. "The NELF pausing checkpoint mediates the functional divergence of Cdk9," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    9. Seina Ohe & Yuji Kubota & Kiyoshi Yamaguchi & Yusuke Takagi & Junichiro Nashimoto & Hiroko Kozuka-Hata & Masaaki Oyama & Yoichi Furukawa & Mutsuhiro Takekawa, 2022. "ERK-mediated NELF-A phosphorylation promotes transcription elongation of immediate-early genes by releasing promoter-proximal pausing of RNA polymerase II," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    10. Annkatrin Bressin & Olga Jasnovidova & Mirjam Arnold & Elisabeth Altendorfer & Filip Trajkovski & Thomas A. Kratz & Joanna E. Handzlik & Denes Hnisz & Andreas Mayer, 2023. "High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    11. Tatsuo Yanagisawa & Yuko Murayama & Haruhiko Ehara & Mie Goto & Mari Aoki & Shun-ichi Sekine, 2024. "Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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