Letter | Published:

UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair

Nature Genetics volume 44, pages 598602 (2012) | Download Citation

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Abstract

Transcription-coupled nucleotide-excision repair (TC-NER) is a subpathway of NER that efficiently removes the highly toxic RNA polymerase II blocking lesions in DNA. Defective TC-NER gives rise to the human disorders Cockayne syndrome and UV-sensitive syndrome (UVSS)1. NER initiating factors are known to be regulated by ubiquitination2. Using a SILAC-based proteomic approach, we identified UVSSA (formerly known as KIAA1530) as part of a UV-induced ubiquitinated protein complex. Knockdown of UVSSA resulted in TC-NER deficiency. UVSSA was found to be the causative gene for UVSS, an unresolved NER deficiency disorder3. The UVSSA protein interacts with elongating RNA polymerase II, localizes specifically to UV-induced lesions, resides in chromatin-associated TC-NER complexes and is implicated in stabilizing the TC-NER master organizing protein ERCC6 (also known as CSB) by delivering the deubiquitinating enzyme USP7 to TC-NER complexes. Together, these findings indicate that UVSSA-USP7–mediated stabilization of ERCC6 represents a critical regulatory mechanism of TC-NER in restoring gene expression.

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References

  1. 1.

    & Transcription-coupled DNA repair: two decades of progress and surprises. Nat. Rev. Mol. Cell Biol. 9, 958–970 (2008).

  2. 2.

    , & Regulation of UV-induced DNA damage response by ubiquitylation. DNA Repair (Amst.) 6, 1231–1242 (2007).

  3. 3.

    , & A new UV-sensitive syndrome not belonging to any complementation groups of xeroderma pigmentosum or Cockayne syndrome: siblings showing biochemical characteristics of Cockayne syndrome without typical clinical manifestations. Mutat. Res. 314, 233–248 (1994).

  4. 4.

    DNA damage, aging, and cancer. N. Engl. J. Med. 361, 1475–1485 (2009).

  5. 5.

    et al. Transcription-dependent cytosine deamination is a novel mechanism in ultraviolet light–induced mutagenesis. Curr. Biol. 20, 170–175 (2010).

  6. 6.

    et al. UV-induced ubiquitylation of XPC protein mediated by UV-DDB–ubiquitin ligase complex. Cell 121, 387–400 (2005).

  7. 7.

    , , , & Sequential binding of UV DNA damage binding factor and degradation of the p48 subunit as early events after UV irradiation. Nucleic Acids Res. 30, 2588–2598 (2002).

  8. 8.

    et al. UV-induced ubiquitination of RNA polymerase II: a novel modification deficient in Cockayne syndrome cells. Proc. Natl. Acad. Sci. USA 93, 11586–11590 (1996).

  9. 9.

    et al. CSA-dependent degradation of CSB by the ubiquitin-proteasome pathway establishes a link between complementation factors of the Cockayne syndrome. Genes Dev. 20, 1429–1434 (2006).

  10. 10.

    , & Damage-induced ubiquitylation of human RNA polymerase II by the ubiquitin ligase Nedd4, but not Cockayne syndrome proteins or BRCA1. Mol. Cell 28, 386–397 (2007).

  11. 11.

    , & Production and characterization of monoclonal antibodies specific to multi-ubiquitin chains of polyubiquitinated proteins. FEBS Lett. 349, 173–180 (1994).

  12. 12.

    , , , & Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res. 7, 143–150 (2000).

  13. 13.

    , , , & STAM proteins bind ubiquitinated proteins on the early endosome via the VHS domain and ubiquitin-interacting motif. Mol. Biol. Cell 14, 3675–3689 (2003).

  14. 14.

    , & DUFs: families in search of function. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66, 1148–1152 (2010).

  15. 15.

    et al. Anti-tumour compounds illudin S and Irofulven induce DNA lesions ignored by global repair and exclusively processed by transcription- and replication-coupled repair pathways. DNA Repair (Amst.) 1, 1027–1038 (2002).

  16. 16.

    , , & A semi-automated non-radioactive system for measuring recovery of RNA synthesis and unscheduled DNA synthesis using ethynyluracil derivatives. DNA Repair (Amst.) 9, 506–516 (2010).

  17. 17.

    UV-sensitive syndrome. Mutat. Res. 577, 162–169 (2005).

  18. 18.

    et al. Complete absence of Cockayne syndrome group B gene product gives rise to UV-sensitive syndrome but not Cockayne syndrome. Proc. Natl. Acad. Sci. USA 101, 15410–15415 (2004).

  19. 19.

    et al. A UV-sensitive syndrome patient with a specific CSA mutation reveals separable roles for CSA in response to UV and oxidative DNA damage. Proc. Natl. Acad. Sci. USA 106, 6209–6214 (2009).

  20. 20.

    et al. Mutations in UVSSA cause UV-sensitive syndrome and destabilize ERCC6 in transcription-coupled DNA repair. Nat. Genet. published online (1 April 2012); doi:10.1038ng.2228.

  21. 21.

    et al. Mutations in UVSSA cause UV-sensitive syndrome and impair RNA polymerase IIo processing in transcription-coupled nucleotide-excision repair. Nat. Genet. published online (1 April 2012); doi:10.1038ng.2229.

  22. 22.

    et al. Activation of multiple DNA repair pathways by sub-nuclear damage induction methods. J. Cell Sci. 120, 2731–2740 (2007).

  23. 23.

    et al. Sequential assembly of the nucleotide excision repair factors in vivo. Mol. Cell 8, 213–224 (2001).

  24. 24.

    , & The transcription cycle of RNA polymerase II in living cells. J. Cell Biol. 159, 777–782 (2002).

  25. 25.

    et al. DNA damage stabilizes interaction of CSB with the transcription elongation machinery. J. Cell Biol. 166, 27–36 (2004).

  26. 26.

    , , & Cockayne syndrome A and B proteins differentially regulate recruitment of chromatin remodeling and repair factors to stalled RNA polymerase II in vivo. Mol. Cell 23, 471–482 (2006).

  27. 27.

    , , , & USP7 counteracts SCFβTrCP- but not APCCdh1-mediated proteolysis of Claspin. J. Cell Biol. 184, 13–19 (2009).

  28. 28.

    , , & USP7/HAUSP stimulates repair of oxidative DNA lesions. Nucleic Acids Res. 39, 2604–2609 (2011).

  29. 29.

    et al. Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature 416, 648–653 (2002).

  30. 30.

    et al. Loss of HAUSP-mediated deubiquitination contributes to DNA damage-induced destabilization of Hdmx and Hdm2. Mol. Cell 18, 565–576 (2005).

  31. 31.

    et al. BRCA1 contributes to transcription-coupled repair of DNA damage through polyubiquitination and degradation of Cockayne syndrome B protein. Cancer Sci. 102, 1840–1847 (2011).

  32. 32.

    & The multifaceted roles of USP7: new therapeutic opportunities. Cell Biochem. Biophys. 60, 61–68 (2011).

  33. 33.

    & Host cell reactivation of plasmids containing oxidative DNA lesions is defective in Cockayne syndrome but normal in UV-sensitive syndrome fibroblasts. DNA Repair (Amst.) 5, 13–22 (2006).

  34. 34.

    et al. The role of CSA in the response to oxidative DNA damage in human cells. Oncogene 26, 4336–4343 (2007).

  35. 35.

    et al. Retinal degeneration and ionizing radiation hypersensitivity in a mouse model for Cockayne syndrome. Mol. Cell. Biol. 27, 1433–1441 (2007).

  36. 36.

    , , , & An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome. PLoS Genet. 4, e1000031 (2008).

  37. 37.

    et al. A versatile viral system for expression and depletion of proteins in mammalian cells. PLoS ONE 4, e6529 (2009).

  38. 38.

    et al. TSPYL5 suppresses p53 levels and function by physical interaction with USP7. Nat. Cell Biol. 13, 102–108 (2011).

  39. 39.

    , & Mammalian cell lines expressing functional RNA polymerase II tagged with the green fluorescent protein. J. Cell Sci. 113, 2679–2683 (2000).

  40. 40.

    et al. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379, 466–469 (1996).

  41. 41.

    et al. A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat. Protoc. 4, 698–705 (2009).

  42. 42.

    et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794–1805 (2011).

  43. 43.

    , , & Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383–5392 (2002).

  44. 44.

    , , & A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646–4658 (2003).

  45. 45.

    & Macromolecular dynamics in living cell nuclei revealed by fluorescence redistribution after photobleaching. Histochem. Cell Biol. 115, 13–21 (2001).

  46. 46.

    et al. Nucleotide excision repair–induced H2A ubiquitination is dependent on MDC1 and RNF8 and reveals a universal DNA damage response. J. Cell Biol. 186, 835–847 (2009).

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Acknowledgements

We thank R. Bernards and M. Epping (Nederlands Kanker Instituut) for the Myc-tagged USP7 expression construct and P. Verrijzer and A. Reddy (Erasmus Medical Centre) for shUSP7-expressing lentivirus. We thank H. Slor (Tel Aviv University) for the TA-24sv40 cell line and N.G.J. Jaspers and H. Lans for discussions and critical reading of the manuscript. This work was funded by the Netherlands Genomics Initiative NPCII (to P.S.), 935.19.021 and 935.11.042 (to W.V., C.L. and J.A.M.), the Dutch Organization for Scientific Research ZonMW Veni Grant (917.96.120 to J.A.M.) and TOP grant (912.08.031 to W.V.), Marie Curie FP7-PIEF-GA-2009-253544 (to M.F.), the Association for International Cancer Research (10-594 to W.V.) and the Cancer Genomics Centre and ERC (advanced research grant to J.H.J.H.).

Author information

Affiliations

  1. Department of Genetics and Netherlands Proteomics Centre, Centre for Biomedical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands.

    • Petra Schwertman
    • , Anja Raams
    • , Adriana C van der Hoek
    • , Charlie Laffeber
    • , Jan H J Hoeijmakers
    • , Wim Vermeulen
    •  & Jurgen A Marteijn
  2. Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre Alexander Fleming, Athens, Greece.

    • Anna Lagarou
    •  & Maria Fousteri
  3. Proteomics Centre, Erasmus University Medical Centre, Rotterdam, The Netherlands.

    • Dick H W Dekkers
    •  & Jeroen A A Demmers

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Contributions

D.H.W.D. and J.A.A.D. performed the mass spectrometry analyses, A.R. performed UDS and RRS experiments, A.C.v.d.H. performed immunoprecipitation experiments, C.L. provided technical assistance, and M.F. designed and, together with A.L., performed ChIP experiments. J.H.J.H. provided support and advice, and helped write the manuscript. P.S. and J.A.M. performed experiments and generated reagents. W.V. and J.A.M. designed the study and supervised the project. W.V., J.A.M. and P.S. wrote the manuscript. All authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Wim Vermeulen or Jurgen A Marteijn.

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DOI

https://doi.org/10.1038/ng.2230

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