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Systematic characterization of deubiquitylating enzymes for roles in maintaining genome integrity

Nature Cell Biology volume 16, pages 10161026 (2014) | Download Citation

Abstract

DNA double-strand breaks (DSBs) are perhaps the most toxic of all DNA lesions, with defects in the DNA-damage response to DSBs being associated with various human diseases. Although it is known that DSB repair pathways are tightly regulated by ubiquitylation, we do not yet have a comprehensive understanding of how deubiquitylating enzymes (DUBs) function in DSB responses. Here, by carrying out a multidimensional screening strategy for human DUBs, we identify several with hitherto unknown links to DSB repair, the G2/M DNA-damage checkpoint and genome-integrity maintenance. Phylogenetic analyses reveal functional clustering within certain DUB subgroups, suggesting evolutionally conserved functions and/or related modes of action. Furthermore, we establish that the DUB UCHL5 regulates DSB resection and repair by homologous recombination through protecting its interactor, NFRKB, from degradation. Collectively, our findings extend the list of DUBs promoting the maintenance of genome integrity, and highlight their potential as therapeutic targets for cancer.

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Acknowledgements

We thank all members of the S.P.J. laboratory for helpful discussions. We are grateful to A. Blackford, D. Larrieu and K. Dry for commenting on the manuscript, N. Lawrence and A. Sossick for help with microscopy, and C. Green for scientific advice. Research in the S.P.J. laboratory is funded by Cancer Research UK Program Grant C6/A11224, the European Research Council and the European Community Seventh Framework Program grant agreement no. HEALTH-F2-2010-259893 (DDResponse). Core infrastructure funding was provided by Cancer Research UK Grant C6946/A14492 and Wellcome Trust Grant WT092096. S.P.J. receives a salary from the University of Cambridge, supplemented by Cancer Research UK. R.N. was funded by a Daiichi Sankyo Foundation of Life Science fellowship and Cancer Research UK Project Grant C6/A14831; C.l.S. was funded by European Molecular Biology Organization Grant ALTF 1165-2010. J.V.F. was supported by Cancer Research UK Program Grant C6/A11224 and the Ataxia Telangiectasia Society.

Author information

Author notes

    • Jorrit Tjeertes

    Present address: Developmental & Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach CH-4002 Basel, Switzerland.

Affiliations

  1. The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK

    • Ryotaro Nishi
    • , Paul Wijnhoven
    • , Carlos le Sage
    • , Jorrit Tjeertes
    • , Yaron Galanty
    • , Josep V. Forment
    •  & Stephen P. Jackson
  2. Cellular & Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, UK

    • Michael J. Clague
    •  & Sylvie Urbé
  3. The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK

    • Stephen P. Jackson

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Contributions

R.N. designed experiments through discussion with P.W., J.T., C.l.S., Y.G. and S.P.J.; P.W., R.N., M.J.C. and S.U. cloned human DUBs. R.N., P.W., C.l.S. and J.T. carried out the screens. P.W. and C.l.S. carried out cell cycle analyses. R.N. carried out most of the other studies with P.W.’s assistance. R.N. and S.P.J. wrote the paper. All other authors, especially P.W., commented and suggested revisions for the paper.

Competing interests

S.P.J. is a founder and shareholder of MISSION Therapeutics Ltd., which is developing DUB inhibitors for therapeutic applications. The other authors declare no competing financial interests.

Corresponding author

Correspondence to Stephen P. Jackson.

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DOI

https://doi.org/10.1038/ncb3028

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