Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Molecular characterization of inter-telomere and intra-telomere mutations in human ALT cells


Telomeres in most immortal cells1,2,3 are maintained by the enzyme telomerase4, allowing cells to divide indefinitely. Some telomerase-negative tumors and immortal cell lines maintain long heterogeneous telomeres by the ALT (alternative lengthening of telomeres) mechanism5,6; such tumors are expected to be resistant to anti-telomerase drug therapies. Occasionally telomerase-negative Saccharomyces cerevisiae mutants survive, and 10% of them (type II survivors) have unstable telomeres7,8. As in human ALT+ cells9, short telomeres in yeast type II survivors lengthen abruptly; in yeast, this is dependent on the recombination proteins Rad52p and Rad50p10. In human cells, ALT involves copying of sequence from a donor to a recipient telomere11. We have characterized for the first time a class of complex telomere mutations seen only in ALT+ cells. The mutant telomeres are defined by the replacement of the progenitor telomere at a discrete point (fusion point) with a different telomere repeat array. Among 19 characterized fusion points, one occurred within the first six repeats of the telomere, indicating that these recombination-like events can occur anywhere within the telomere. One mutant telomere may have been involved in a secondary recombination-like mutation event, suggesting that these mutations are sporadic but ongoing in ALT+ cells. We also identified simple intra-allelic mutations at high frequency, which evidently contribute to telomere instability in ALT+ cells.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: The principle of TVR–PCR, and comparison of IIICF/a2 ALT– and ALT+ telomere maps.
Figure 2: Example of a mutation in the 12qΔ telomere in a WI-38 ALT+ clone.
Figure 3: Alignment of the ten mutant 12qΔ telomere codes from WI-38 ALT+ clones with the progenitor allele.


  1. Morin, G.B. The human telomere terminal transferase enzyme is a ribonucleoprotein that synthesizes TTAGGG repeats. Cell 59, 521–529 (1989).

    Article  CAS  PubMed  Google Scholar 

  2. Kim, N.W. et al. Specific association of human telomerase activity with immortal cells and cancer. Science 266, 2011–2015 (1994).

    Article  CAS  PubMed  Google Scholar 

  3. Wright, W.E., Piatyszek, M.A., Rainey, W.E., Byrd, W. & Shay, J.W. Telomerase activity in human germline and embryonic-tissues and cells. Dev. Genet. 18, 173–179 (1996).

    Article  CAS  PubMed  Google Scholar 

  4. Greider, C.W. & Blackburn, E.H. Identification of a specific telomere terminal transferase activity in Tetrahymena extracts. Cell 43, 405–413 (1985).

    Article  CAS  PubMed  Google Scholar 

  5. Bryan, T.M., Englezou, A., Gupta, J., Bacchetti, S. & Reddel, R.R. Telomere elongation in immortal human cells without detectable telomerase activity. EMBO J. 14, 4240–4248 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Bryan, T.M., Englezou, A., Dalla-Pozza, L., Dunham, M.A. & Reddel, R.R. Evidence for an alternative mechanism for maintaining telomere length in human tumors and tumor-derived cell lines. Nature Med. 3, 1271–1274 (1997).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Murnane, J.P., Sabatier, L., Marder, B.A. & Morgan, W.F. Telomere dynamics in an immortal human cell line. EMBO J. 13, 4953–4962 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Teng, C.S., Chang, J., McCowan, B. & Zakian, A.V. Telomerase-independent lengthening of yeast telomeres occurs by an abrupt Rad50p-dependent, Rif-inhibited recombinational process. Mol. Cell 6, 947–952 (2000).

    Article  CAS  PubMed  Google Scholar 

  11. 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).

    Article  CAS  PubMed  Google Scholar 

  12. Allsopp, R.C. et al. Telomere length predicts replicative capacity of human fibroblasts. Proc. Natl Acad. Sci. USA 89, 10114–10118 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Allsopp, R.C. & Harley, C.B. Evidence for a critical telomere length in senescent human fibroblasts. Exp. Cell Res. 219, 130–136 (1995).

    Article  CAS  PubMed  Google Scholar 

  14. Counter, C.M. et al. Telomere shortening associated with chromosome instability is arrested in immortal cells which express telomerase activity. EMBO J. 11, 1921–1929 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Counter, C.M., Botelho, F.M., Wang, P., Harley, C.B. & Bacchetti, S. Stabilization of short telomeres and telomerase activity accompany immortalization of Epstein-Barr virus-transformed human B lymphocytes. J. Virol. 68, 3410–3414 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Bryan, T.M. & Reddel, R.R. Telomere dynamics and telomerase activity in in vitro immortalised human cells. Eur. J. Cancer 33, 767–773 (1997).

    Article  CAS  PubMed  Google Scholar 

  17. Allshire, R.C., Dempster, M. & Hastie, N.D. Human telomeres contain at least three types of G-rich repeat distributed non-randomly. Nucleic Acids Res. 17, 4611–4627 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Baird, D.M., Jeffreys, A.J. & Royle, N.J. Mechanisms underlying telomere repeat turnover, revealed by hypervariable variant repeat distribution patterns in the human X/Yp telomere. EMBO J. 14, 5433–5443 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Baird, D.M., Coleman, J., Rosser, Z.H. & Royle, N.J. High levels of sequence polymorphism and linkage disequilibrium at the telomere of 12q: implications for telomere biology and human evolution. Am. J. Hum. Genet. 66, 235–250 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Coleman, J., Baird, D.M. & Royle, N.J. The plasticity of human telomeres demonstrated by a hypervariable telomere repeat array that is located on some copies of 16p and 16q. Hum. Mol. Genet. 8, 1637–1646 (1999).

    Article  CAS  PubMed  Google Scholar 

  21. Yeager, T.R. et al. Telomerase-negative immortalized human cells contain a novel type of promyelocytic leukemia (PML) body. Cancer Res. 59, 4175–4179 (1999).

    CAS  PubMed  Google Scholar 

  22. Rizki, A. & Lundblad, V. Defects in mismatch repair promote telomerase-independent proliferation. Nature 411, 713–716 (2001).

    Article  CAS  PubMed  Google Scholar 

  23. Warneford, S.G. et al. Germ-line splicing mutation of the p53 gene in a cancer-prone family. Cell Growth Differ. 3, 839–846 (1992).

    CAS  PubMed  Google Scholar 

  24. Rogan, E.M. et al. Alterations in p53 and p16INK4 expression and telomere length during spontaneous immortalization of Li-Fraumeni syndrome fibroblasts. Mol. Cell. Biol. 15, 4745–4753 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Ford, L.P. et al. Telomerase can inhibit the recombination-based pathway of telomere maintenance in human cells. J. Biol. Chem. 276, 32198–32203 (2001).

    Article  CAS  PubMed  Google Scholar 

  26. Bryan, T.M., Marusic, L., Bacchetti, S., Namba, M. & Reddel, R.R. The telomere lengthening mechanism in telomerase-negative immortal human cells does not involve the telomerase RNA subunit. Hum. Mol. Genet. 6, 921–926 (1997).

    Article  CAS  PubMed  Google Scholar 

  27. Jeffreys, A.J., Macleod, A., Tamaki, K., Neil, D.L. & Monckton, D.G. Minisatellite repeat coding as a digital approach to DNA typing. Nature 354, 204–209 (1991).

    Article  CAS  PubMed  Google Scholar 

  28. Baird, D.M. & Royle, N.J. Sequences from higher primates orthologous to the human Xp/Yp telomere junction region reveal gross rearrangements and high levels of divergence. Hum. Mol. Genet. 6, 2291–2299 (1997).

    Article  CAS  PubMed  Google Scholar 

Download references


We thank A.J. Jeffreys and C. May for their valuable comments on the manuscript. The work was funded by a UK Medical Research Council component group grant (to N.J.R.) and funding (to R.R.) from the Carcinogenesis Fellowship of the New South Wales Cancer Council. H.A.P. was supported by a UK-MRC studentship.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Nicola J. Royle.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Varley, H., Pickett, H., Foxon, J. et al. Molecular characterization of inter-telomere and intra-telomere mutations in human ALT cells. Nat Genet 30, 301–305 (2002).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing