Letter

Structural basis for the initiation of eukaryotic transcription-coupled DNA repair

Received:
Accepted:
Published online:

Abstract

Eukaryotic transcription-coupled repair (TCR) is an important and well-conserved sub-pathway of nucleotide excision repair that preferentially removes DNA lesions from the template strand that block translocation of RNA polymerase II (Pol II)1,2. Cockayne syndrome group B (CSB, also known as ERCC6) protein in humans (or its yeast orthologues, Rad26 in Saccharomyces cerevisiae and Rhp26 in Schizosaccharomyces pombe) is among the first proteins to be recruited to the lesion-arrested Pol II during the initiation of eukaryotic TCR1,3,4,5,6,7,8,9,10. Mutations in CSB are associated with the autosomal-recessive neurological disorder Cockayne syndrome, which is characterized by progeriod features, growth failure and photosensitivity1. The molecular mechanism of eukaryotic TCR initiation remains unclear, with several long-standing unanswered questions. How cells distinguish DNA lesion-arrested Pol II from other forms of arrested Pol II, the role of CSB in TCR initiation, and how CSB interacts with the arrested Pol II complex are all unknown. The lack of structures of CSB or the Pol II–CSB complex has hindered our ability to address these questions. Here we report the structure of the S. cerevisiae Pol II–Rad26 complex solved by cryo-electron microscopy. The structure reveals that Rad26 binds to the DNA upstream of Pol II, where it markedly alters its path. Our structural and functional data suggest that the conserved Swi2/Snf2-family core ATPase domain promotes the forward movement of Pol II, and elucidate key roles for Rad26 in both TCR and transcription elongation.

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Acknowledgements

We thank the Wang and Leschziner laboratories for discussions. D.W., A.E.L. and P.B.D. were supported by National Institutes of Health (NIH) grants GM102362, GM102362-S1 (D.W.), GM092895 (A.E.L.), and GM27681 (P.B.D.). M.A.C. acknowledges support from the Damon Runyon Cancer Research Foundation. We thank the UCSD cryo-EM Facility, where all data was collected. We used the Extreme Science and Engineering Discovery Environment (XSEDE) for computing allocations (MCB160121 to D.W.), supported by NSF grant ACI-1548562.

Author information

Author notes

    • Michael A. Cianfrocco

    Present address: Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.

    • Jun Xu
    •  & Indrajit Lahiri

    These authors contributed equally to this work.

    • Andres E. Leschziner
    •  & Dong Wang

    These authors jointly supervised this work.

Affiliations

  1. Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA

    • Jun Xu
    • , Wei Wang
    • , Jenny Chong
    •  & Dong Wang
  2. Department of Cellular & Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093, USA

    • Indrajit Lahiri
    • , Adam Wier
    • , Michael A. Cianfrocco
    • , Andres E. Leschziner
    •  & Dong Wang
  3. Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA

    • Alissa A. Hare
    •  & Peter B. Dervan
  4. Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA

    • Frank DiMaio
  5. Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA

    • Andres E. Leschziner

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Contributions

J.X. prepared the proteins with help from W.W. and J.C. and performed the biochemical analyses. A.H. and P.D.B. provided the Py-Im chemical agent. I. L. collected the EM data with help from A.W. I.L. performed data processing and refinement with help from M.A.C. I.L. and F.D. generated the atomic models with homology models generated by J.X., W.W. and D.W. D.W. and A.E.L. wrote the manuscript with help from all laboratory members. D.W. and A.E.L. directed and supervised the research.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Andres E. Leschziner or Dong Wang.

Reviewer Information Nature thanks A. Conconi and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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    Supplementary Information

    This file contains Supplementary Figure 1, the gel source data and Supplementary Tables 1-2.

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