HAATI survivors replace canonical telomeres with blocks of generic heterochromatin

Abstract

The notion that telomeres are essential for chromosome linearity stems from the existence of two chief dangers: inappropriate DNA damage response (DDR) reactions that mistake natural chromosome ends for double-strand DNA breaks (DSBs), and the progressive loss of DNA from chromosomal termini due to the end replication problem. Telomeres avert the former peril by binding sequence-specific end-protection factors that control the access of DDR activities1,2. The latter threat is tackled by recruiting telomerase, a reverse transcriptase that uses an integral RNA subunit to template the addition of telomere repeats to chromosome ends3. Here we describe an alternative mode of linear chromosome maintenance in which canonical telomeres are superseded by blocks of heterochromatin. We show that in the absence of telomerase, Schizosaccharomyces pombe cells can survive telomere sequence loss by continually amplifying and rearranging heterochromatic sequences. Because the heterochromatin assembly machinery is required for this survival mode, we have termed it ‘HAATI’ (heterochromatin amplification-mediated and telomerase-independent). HAATI uses the canonical end-protection protein Pot1 (ref. 4) and its interacting partner Ccq1 (ref. 5) to preserve chromosome linearity. The data suggest a model in which Ccq1 is recruited by the amplified heterochromatin and provides an anchor for Pot1, which accomplishes its end-protection function in the absence of its cognate DNA-binding sequence. HAATI resembles the chromosome end-maintenance strategy found in Drosophila melanogaster, which lacks specific telomere sequences but nonetheless assembles terminal heterochromatin structures that recruit end-protection factors. These findings reveal a previously unrecognized mode by which cancer cells might escape the requirement for telomerase activation, and offer a tool for studying genomes that sustain unusually high levels of heterochromatinization.

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Figure 1: Characterization of HAATI strains.
Figure 2: Trt1 addition reveals extensive genomic rearrangements in HAATI cells.
Figure 3: HAATI survival requires Clr4 and Rhp51.
Figure 4: HAATI strains lack terminal telomere sequences but require Pot1 for end-protection.

References

  1. 1

    Palm, W. & de Lange, T. How shelterin protects mammalian telomeres. Annu. Rev. Genet. 42, 301–334 (2008)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  2. 2

    Rog, O. & Cooper, J. P. Telomeres in drag: dressing as DNA damage to engage telomerase. Curr. Opin. Genet. Dev. 18, 212–220 (2008)

    CAS  PubMed  Article  Google Scholar 

  3. 3

    Blackburn, E. H. Telomeres and telomerase: their mechanisms of action and the effects of altering their functions. FEBS Lett. 579, 859–862 (2005)

    CAS  PubMed  Article  Google Scholar 

  4. 4

    Baumann, P. & Cech, T. R. Pot1, the putative telomere end-binding protein in fission yeast and humans. Science 292, 1171–1175 (2001)

    ADS  CAS  PubMed  Article  Google Scholar 

  5. 5

    Miyoshi, T., Kanoh, J., Saito, M. & Ishikawa, F. Fission yeast Pot1-Tpp1 protects telomeres and regulates telomere length. Science 320, 1341–1344 (2008)

    ADS  CAS  Article  Google Scholar 

  6. 6

    Dunham, M. A., Neumann, A. A., Fasching, C. L. & Reddel, R. R. Telomere maintenance by recombination in human cells. Nature Genet. 26, 447–450 (2000)

    CAS  PubMed  Article  Google Scholar 

  7. 7

    Lundblad, V. & Blackburn, E. H. An alternative pathway for yeast telomere maintenance rescues est1 senescence. Cell 73, 347–360 (1993)

    CAS  PubMed  Article  Google Scholar 

  8. 8

    Teng, S. C. & Zakian, V. A. Telomere-telomere recombination is an efficient bypass pathway for telomere maintenance in Saccharomyces cerevisiae . Mol. Cell. Biol. 19, 8083–8093 (1999)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  9. 9

    McEachern, M. J. & Haber, J. E. Break-induced replication and recombinational telomere elongation in yeast. Annu. Rev. Biochem. 75, 111–135 (2006)

    CAS  PubMed  Article  Google Scholar 

  10. 10

    Maringele, L. & Lydall, D. Telomerase- and recombination-independent immortalization of budding yeast. Genes Dev. 18, 2663–2675 (2004)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  11. 11

    Cooper, J. P., Nimmo, E. R., Allshire, R. C. & Cech, T. R. Regulation of telomere length and function by a Myb-domain protein in fission yeast. Nature 385, 744–747 (1997)

    ADS  CAS  PubMed  Article  Google Scholar 

  12. 12

    Nakamura, T. M., Cooper, J. P. & Cech, T. R. Two modes of survival of fission yeast without telomerase. Science 282, 493–496 (1998)

    ADS  CAS  PubMed  Article  Google Scholar 

  13. 13

    Wang, X. & Baumann, P. Chromosome fusions following telomere loss are mediated by single-strand annealing. Mol. Cell 31, 463–473 (2008)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  14. 14

    Sugawara, N. DNA sequences at the telomeres of the fission yeast S. pombe. PhD thesis, Harvard Univ. (1988)

  15. 15

    Toda, T., Nakaseko, Y., Niwa, O. & Yanagida, M. Mapping of rRNA genes by integration of hybrid plasmids in Schizosaccharomyces pombe . Curr. Genet. 8, 93–97 (1984)

    CAS  PubMed  Article  Google Scholar 

  16. 16

    Cam, H. P. et al. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nature Genet. 37, 809–819 (2005)

    CAS  PubMed  Article  Google Scholar 

  17. 17

    Kanoh, J., Sadaie, M., Urano, T. & Ishikawa, F. Telomere binding protein Taz1 establishes Swi6 heterochromatin independently of RNAi at telomeres. Curr. Biol. 15, 1808–1819 (2005)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  18. 18

    Nakayama, J., Rice, J. C., Strahl, B. D., Allis, C. D. & Grewal, S. I. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292, 110–113 (2001)

    ADS  CAS  PubMed  Article  Google Scholar 

  19. 19

    Ekwall, K. et al. Mutations in the fission yeast silencing factors clr4+ and rik1+ disrupt the localisation of the chromo domain protein Swi6p and impair centromere function. J. Cell Sci. 109, 2637–2648 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20

    Nakamura, K. et al. Rad51 suppresses gross chromosomal rearrangement at centromere in Schizosaccharomyces pombe . EMBO J. 27, 3036–3046 (2008)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  21. 21

    Sugiyama, T. et al. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell 128, 491–504 (2007)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  22. 22

    Tomita, K. & Cooper, J. P. Fission yeast Ccq1 is telomerase recruiter and local checkpoint controller. Genes Dev. 22, 3461–3474 (2008)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  23. 23

    Pitt, C. W. & Cooper, J. P. Pot1 inactivation leads to rampant telomere resection and loss in one cell cycle. Nucleic Acids Res. advance online publication,. 10.1093/nar/gkq580 (3 July 2010)

  24. 24

    Ishii, K. et al. Heterochromatin integrity affects chromosome reorganization after centromere dysfunction. Science 321, 1088–1091 (2008)

    ADS  CAS  PubMed  Article  Google Scholar 

  25. 25

    Allshire, R. C. & Karpen, G. H. Epigenetic regulation of centromeric chromatin: old dogs, new tricks? Nature Rev. Genet. 9, 923–937 (2008)

    CAS  PubMed  Article  Google Scholar 

  26. 26

    Mason, J. M., Frydrychova, R. C. & Biessmann, H. Drosophila telomeres: an exception providing new insights. Bioessays 30, 25–37 (2008)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  27. 27

    Cenci, G., Ciapponi, L. & Gatti, M. The mechanism of telomere protection: a comparison between Drosophila and humans. Chromosoma 114, 135–145 (2005)

    CAS  PubMed  Article  Google Scholar 

  28. 28

    Pardue, M. L. & DeBaryshe, P. G. Retrotransposons provide an evolutionarily robust non-telomerase mechanism to maintain telomeres. Annu. Rev. Genet. 37, 485–511 (2003)

    CAS  PubMed  Article  Google Scholar 

  29. 29

    Cenci, G., Siriaco, G., Raffa, G. D., Kellum, R. & Gatti, M. The Drosophila HOAP protein is required for telomere capping. Nature Cell Biol. 5, 82–84 (2003)

    CAS  PubMed  Article  Google Scholar 

  30. 30

    Gao, G. et al. HipHop interacts with HOAP and HP1 to protect Drosophila telomeres in a sequence-independent manner. EMBO J. 29, 819–829 (2010)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  31. 31

    Haering, C. H., Nakamura, T. M., Baumann, P. & Cech, T. R. Analysis of telomerase catalytic subunit mutants in vivo and in vitro in Schizosaccharomyces pombe . Proc. Natl Acad. Sci. USA 97, 6367–6372 (2000)

    ADS  CAS  PubMed  Article  Google Scholar 

  32. 32

    Moreno, S., Klar, A. & Nurse, P. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe . Methods Enzymol. 194, 795–823 (1991)

    CAS  Article  Google Scholar 

  33. 33

    Tomita, K. & Cooper, J. P. The telomere bouquet controls the meiotic spindle. Cell 130, 113–126 (2007)

    CAS  PubMed  Article  Google Scholar 

  34. 34

    Ferreira, M. G. & Cooper, J. P. The fission yeast Taz1 protein protects chromosomes from Ku-dependent end-to-end fusions. Mol. Cell 7, 55–63 (2001)

    CAS  Article  Google Scholar 

  35. 35

    Miller, K. M., Rog, O. & Cooper, J. P. Semi-conservative DNA replication through telomeres requires Taz1. Nature 440, 824–828 (2006)

    ADS  CAS  Article  Google Scholar 

  36. 36

    Ferreira, M. G. & Cooper, J. P. Two modes of DNA double-strand break repair are reciprocally regulated through the fission yeast cell cycle. Genes Dev. 18, 2249–2254 (2004)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  37. 37

    Tomita, K. et al. Competition between the Rad50 complex and the Ku heterodimer reveals a role for Exo1 in processing double-strand breaks but not telomeres. Mol. Cell. Biol. 23, 5186–5197 (2003)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

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Acknowledgements

We thank T. Cech for discussions and gratefully acknowledge that initial work by T.M.N. on reintroducing Trt1 to circular strains was performed in the Cech laboratory. We thank our current and former laboratory members for discussions and advice. This work was supported by Cancer Research UK.

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Contributions

D.J. performed the experiments in Figs 3 and 4, Supplementary Figs 6 and 9–17 and Supplementary Tables 1 and 2, and reproduced Figs 1a, b, 2a, d and Supplementary Figs 2 and 8a. A.K.H. first isolated HAATI survivors and performed the experiments in Figs 1 and 2b–d, and Supplementary Figs 2, 4, 5 and 8. T.M.N. performed the experiments in Fig. 2a. K.M.M. first showed that circular strains are hypersensitive to DSB-inducing agents. J.P.C. designed and supervised the study. J.P.C. and D.J. generated the figures and wrote the paper.

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Correspondence to Julia Promisel Cooper.

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The authors declare no competing financial interests.

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The file contains Supplementary Figures 1-17 with legends, Supplementary Tables 1-2 and a Strain Table. (PDF 913 kb)

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Jain, D., Hebden, A., Nakamura, T. et al. HAATI survivors replace canonical telomeres with blocks of generic heterochromatin. Nature 467, 223–227 (2010). https://doi.org/10.1038/nature09374

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