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Structural basis of RNA polymerase II backtracking, arrest and reactivation


During gene transcription, RNA polymerase (Pol) II moves forwards along DNA and synthesizes messenger RNA. However, at certain DNA sequences, Pol II moves backwards, and such backtracking can arrest transcription. Arrested Pol II is reactivated by transcription factor IIS (TFIIS), which induces RNA cleavage that is required for cell viability1. Pol II arrest and reactivation are involved in transcription through nucleosomes2,3 and in promoter-proximal gene regulation4,5,6. Here we present X-ray structures at 3.3 Å resolution of an arrested Saccharomyces cerevisiae Pol II complex with DNA and RNA, and of a reactivation intermediate that additionally contains TFIIS. In the arrested complex, eight nucleotides of backtracked RNA bind a conserved ‘backtrack site’ in the Pol II pore and funnel, trapping the active centre trigger loop and inhibiting mRNA elongation. In the reactivation intermediate, TFIIS locks the trigger loop away from backtracked RNA, displaces RNA from the backtrack site, and complements the polymerase active site with a basic and two acidic residues that may catalyse proton transfers during RNA cleavage. The active site is demarcated from the backtrack site by a ‘gating tyrosine’ residue that probably delimits backtracking. These results establish the structural basis of Pol II backtracking, arrest and reactivation, and provide a framework for analysing gene regulation during transcription elongation.

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Figure 1: Structure of arrested Pol II.
Figure 2: Backtracked RNA in the backtrack site.
Figure 3: Structure of reactivation intermediate.
Figure 4: Mechanism of Pol II backtracking, arrest and reactivation.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates and structure factors of the arrested Pol II elongation complex and the arrested Pol II reactivation intermediate have been deposited with the Protein Data Bank under accession numbers 3PO2 and 3PO3, respectively.


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We thank F. Brueckner, G. Damsma, K. Kinkelin, D. Kostrewa, L. Larivière, E. Lehmann, F. Martinez, S. Sainsbury and J. Sydow. Part of this work was performed at the Swiss Light Source at the Paul Scherrer Institut, Villigen, Switzerland. P.C. was supported by the Deutsche Forschungsgemeinschaft, SFB646, TR5, FOR1068, NIM, Bioimaging Network BIN, and the Jung-Stiftung.

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A.C.M.C. carried out experiments. P.C. supervised the project. A.C.M.C. and P.C. prepared the manuscript.

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Correspondence to Patrick Cramer.

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The authors declare no competing financial interests.

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Cheung, A., Cramer, P. Structural basis of RNA polymerase II backtracking, arrest and reactivation. Nature 471, 249–253 (2011).

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