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Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy-1


Spinocerebellar ataxia with axonal neuropathy-1 (SCAN1) is a neurodegenerative disease that results from mutation of tyrosyl phosphodiesterase 1 (TDP1)1. In lower eukaryotes, Tdp1 removes topoisomerase 1 (top1) peptide from DNA termini during the repair of double-strand breaks created by collision of replication forks with top1 cleavage complexes in proliferating cells2,3,4. Although TDP1 most probably fulfils a similar function in human cells, this role is unlikely to account for the clinical phenotype of SCAN1, which is associated with progressive degeneration of post-mitotic neurons. In addition, this role is redundant in lower eukaryotes, and Tdp1 mutations alone confer little phenotype4,5,6,7. Moreover, defects in processing or preventing double-strand breaks during DNA replication are most probably associated with increased genetic instability and cancer, phenotypes not observed in SCAN1 (ref. 8). Here we show that in human cells TDP1 is required for repair of chromosomal single-strand breaks arising independently of DNA replication from abortive top1 activity or oxidative stress. We report that TDP1 is sequestered into multi-protein single-strand break repair (SSBR) complexes by direct interaction with DNA ligase IIIα and that these complexes are catalytically inactive in SCAN1 cells. These data identify a defect in SSBR in a neurodegenerative disease, and implicate this process in the maintenance of genetic integrity in post-mitotic neurons.

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Figure 1: Defective repair of replication-independent top1-SSBs in SCAN1.
Figure 2: Defective repair of top1-SSBs in other SSBR mutant cells.
Figure 3: TDP1 interacts with DNA ligase IIIα and is a component of SSBR multi-protein complexes.
Figure 4: Repair of oxidative SSBs, CPT-induced transcriptional inhibition, and sister chromatid exchanges in SCAN1 cells.


  1. Takashima, H. et al. Mutation of TDP1, encoding a topoisomerase I-dependent DNA damage repair enzyme, in spinocerebellar ataxia with axonal neuropathy. Nature Genet. 32, 267–272 (2002)

    Article  CAS  Google Scholar 

  2. Pouliot, J. J., Yao, K. C., Robertson, C. A. & Nash, H. A. Yeast gene for a Tyr-DNA phosphodiesterase that repairs topoisomerase I complexes. Science 286, 552–555 (1999)

    Article  CAS  Google Scholar 

  3. Li, T. K. & Liu, L. F. Tumor cell death induced by topoisomerase-targeting drugs. Annu. Rev. Pharmacol. Toxicol. 41, 53–77 (2001)

    Article  Google Scholar 

  4. Pouliot, J. J., Robertson, C. A. & Nash, H. A. Pathways for repair of topoisomerase I covalent complexes in Saccharomyces cerevisiae . Genes Cells 6, 677–687 (2001)

    Article  CAS  Google Scholar 

  5. Liu, C., Pouliot, J. J. & Nash, H. A. Repair of topoisomerase I covalent complexes in the absence of the tyrosyl-DNA phosphodiesterase Tdp1. Proc. Natl Acad. Sci. USA 99, 14970–14975 (2002)

    Article  ADS  CAS  Google Scholar 

  6. Vance, J. R. & Wilson, T. E. Yeast Tdp1 and Rad1-Rad10 function as redundant pathways for repairing Top1 replicative damage. Proc. Natl Acad. Sci. USA 99, 13669–13674 (2002)

    Article  ADS  CAS  Google Scholar 

  7. Liu, C., Pouliot, J. J. & Nash, H. A. The role of TDP1 from budding yeast in the repair of DNA damage. DNA Repair (Amst.) 3, 593–601 (2004)

    Article  CAS  Google Scholar 

  8. Shivji, M. K. & Venkitaraman, A. R. DNA recombination, chromosomal stability and carcinogenesis: insights into the role of BRCA2. DNA Repair (Amst.) 3, 835–843 (2004)

    Article  CAS  Google Scholar 

  9. Hsiang, Y. H., Hertzberg, R., Hecht, S. & Liu, L. F. Camptothecin induces protein-linked DNA breaks via mammalian DNA topoisomerase I. J. Biol. Chem. 260, 14873–14878 (1985)

    CAS  PubMed  Google Scholar 

  10. Fairbairn, D. W., Olive, P. L. & O'Neill, K. L. The comet assay: a comprehensive review. Mutat. Res. 339, 37–59 (1995)

    Article  CAS  Google Scholar 

  11. Bendixen, C., Thomsen, B., Alsner, J. & Westergaard, O. Camptothecin-stabilized topoisomerase I-DNA adducts cause premature termination of transcription. Biochemistry 29, 5613–5619 (1990)

    Article  CAS  Google Scholar 

  12. Pommier, Y. et al. Repair of and checkpoint response to topoisomerase I-mediated DNA damage. Mutat. Res. 532, 173–203 (2003)

    Article  CAS  Google Scholar 

  13. Wu, J. & Liu, L. F. Processing of topoisomerase I cleavable complexes into DNA damage by transcription. Nucleic Acids Res. 25, 4181–4186 (1997)

    Article  CAS  Google Scholar 

  14. Caldecott, K. W., Tucker, J. D., Stanker, L. H. & Thompson, L. H. Characterization of the XRCC1-DNA ligase III complex in vitro and its absence from mutant hamster cells. Nucleic Acids Res. 23, 4836–4843 (1995)

    Article  CAS  Google Scholar 

  15. Rasouli-Nia, A., Karimi-Busheri, F. & Weinfeld, M. Stable down-regulation of human polynucleotide kinase enhances spontaneous mutation frequency and sensitizes cells to genotoxic agents. Proc. Natl Acad. Sci. USA 101, 6905–6910 (2004)

    Article  ADS  CAS  Google Scholar 

  16. Caldecott, K. W. XRCC1 and DNA strand break repair. DNA Repair (Amst.) 2, 955–969 (2003)

    Article  CAS  Google Scholar 

  17. Loizou, J. I. et al. The protein kinase CK2 facilitates repair of chromosomal DNA single-strand breaks. Cell 117, 17–28 (2004)

    Article  CAS  Google Scholar 

  18. Whitehouse, C. J. et al. XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair. Cell 104, 1–11 (2001)

    Article  Google Scholar 

  19. O'Driscoll, M. et al. DNA ligase IV mutations identified in patients exhibiting developmental delay and immunodeficiency. Mol. Cell 8, 1175–1185 (2001)

    Article  CAS  Google Scholar 

  20. Caldecott, K. W., Mckeown, C. K., Tucker, J. D., Ljungquist, S. & Thompson, L. H. An interaction between the mammalian DNA repair protein XRCC1 and DNA ligase III. Mol. Cell. Biol. 14, 68–76 (1994)

    Article  CAS  Google Scholar 

  21. Moore, D. J., Taylor, R. M., Clements, P. & Caldecott, K. W. Mutation of a BRCT domain selectively disrupts DNA single-strand break repair in noncycling Chinese hamster ovary cells. Proc. Natl Acad. Sci. USA 97, 13649–13654 (2000)

    Article  ADS  CAS  Google Scholar 

  22. Taylor, R. M., Moore, D. J., Whitehouse, J., Johnson, P. & Caldecott, K. W. A cell cycle-specific requirement for the XRCC1 BRCT II domain during mammalian DNA strand break repair. Mol. Cell. Biol. 20, 735–740 (2000)

    Article  CAS  Google Scholar 

  23. Plo, I. et al. Association of XRCC1 and tyrosyl DNA phosphodiesterase (Tdp1) for the repair of topoisomerase I-mediated DNA lesions. DNA Repair (Amst.) 2, 1087–1100 (2003)

    Article  CAS  Google Scholar 

  24. Pourquier, P. et al. Induction of reversible complexes between eukaryotic DNA topoisomerase I and DNA-containing oxidative base damages. 7, 8-dihydro-8-oxoguanine and 5-hydroxycytosine. J. Biol. Chem. 274, 8516–8523 (1999)

    Article  CAS  Google Scholar 

  25. Inamdar, K. V. et al. Conversion of phosphoglycolate to phosphate termini on 3′ overhangs of DNA double strand breaks by the human tyrosyl-DNA phosphodiesterase hTdp1. J. Biol. Chem. 277, 27162–27168 (2002)

    Article  CAS  Google Scholar 

  26. Bradley, M. O. & Kohn, K. W. X-ray induced DNA double strand break production and repair in mammalian cells as measured by neutral filter elution. Nucleic Acids Res. 7, 793–804 (1979)

    Article  CAS  Google Scholar 

  27. Kathe, S. D., Shen, G. P. & Wallace, S. S. Single-stranded breaks in DNA but not oxidative DNA base damages block transcriptional elongation by RNA polymerase II in HeLa cell nuclear extracts. J. Biol. Chem. 279, 18511–18520 (2004)

    Article  CAS  Google Scholar 

  28. Zhou, W. & Doetsch, P. W. Transcription bypass or blockage at single-strand breaks on the DNA template strand: effect of different 3′ and 5′ flanking groups on the T7 RNA polymerase elongation complex. Biochemistry 33, 14926–14934 (1994)

    Article  CAS  Google Scholar 

  29. Perry, P. & Wolff, S. New Giemsa method for the differential staining of sister chromatids. Nature 251, 156–158 (1974)

    Article  ADS  CAS  Google Scholar 

  30. Lambert, S. & Lopez, B. S. Role of RAD51 in sister-chromatid exchanges in mammalian cells. Oncogene 20, 6627–6631 (2001)

    Article  CAS  Google Scholar 

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We thank M. Withers and L. Ju for technical assistance, H. Nash for tyrosine oligonucleotide and critical reading of the manuscript, F. Karimi-Busheri and A. Rasouli-Nia for C-ter3 cells. This work was supported by an MRC Programme Grant to K.W.C. and by an Overseas Research Scholarship and a Stapley Trust award to S.F.E-K.

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Correspondence to Keith W. Caldecott.

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Supplementary information

Supplementary Figure 1

Depicts the use of alkaline unwinding to measure strand breaks in normal and SCAN1 cells. (PPT 26 kb)

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El-Khamisy, S., Saifi, G., Weinfeld, M. et al. Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy-1. Nature 434, 108–113 (2005).

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