Alternative lengthening of telomeres: models, mechanisms and implications

Key Points

  • About 10% of all cancers, including some that have a particularly poor prognosis, use the alternative lengthening of telomeres (ALT) pathway to prevent the telomere shortening that accompanies proliferation of normal cells.

  • ALT-positive cells commonly have a number of unusual characteristics, including telomeric DNA that is separated from chromosome ends. This extrachromosomal telomeric DNA may be linear or circular.

  • Partially single-stranded circles of telomeric DNA in which the C-rich (AATCCC)n strand is essentially intact and the G-rich (TTAGGG)n strand is gapped seem to be the best of the known markers for ALT. The quantity of this 'C-circle' DNA correlates well with the amount of ALT activity.

  • Telomere elongation in ALT cells involves homologous recombination.

  • The experimental evidence fits best with a model for ALT in which telomeric 3′ overhangs become extended by invading other telomeric DNA and using it as a template for DNA replication. The other telomeric DNA can be: part of the same telomere (through telomere-loop formation); in a sister chromatid; in the telomere of another chromosome; or in one of the forms of extrachromosomal telomeric DNA.

  • Proteins that are thought to be required for ALT include the homologous recombination protein complexes MRN (which is made up of meiotic recombination 11 (MRE11, also known as MRE11A), RAD50 and Nijmegen breakage syndrome 1 (NBS1, also known as NBN)) and structural maintenance of chromosomes 5 (SMC5)–SMC6, and proteins, such as flap endonuclease 1 (FEN1), MUS81, Fanconi anaemia group D2 (FANCD2) and Fanconi anaemia group A (FANCA), that may be required for recombination-dependent restart of stalled telomeric DNA replication.

  • Promyelocytic leukaemia (PML) bodies containing telomeric DNA are characteristic of ALT cells, and are referred to as ALT-associated PML bodies (APBs). Large APBs seem to be associated with senescence of ALT cells and sequestration of extrachromosomal DNA, but we speculate that smaller APBs may be sites at which telomere lengthening occurs.

  • In ALT cells, many of the telomeres elicit a DNA-damage response but repress chromosome end-to-end fusions. This telomere state, which is intermediate between the fully capped and uncapped fusogenic telomere states, may reflect a structural change that is permissive for recombination-mediated telomere replication.

Abstract

Unlimited cellular proliferation depends on counteracting the telomere attrition that accompanies DNA replication. In human cancers this usually occurs through upregulation of telomerase activity, but in 10–15% of cancers — including some with particularly poor outcome — it is achieved through a mechanism known as alternative lengthening of telomeres (ALT). ALT, which is dependent on homologous recombination, is therefore an important target for cancer therapy. Although dissection of the mechanism or mechanisms of ALT has been challenging, recent advances have led to the identification of several genes that are required for ALT and the elucidation of the biological significance of some phenotypic markers of ALT. This has enabled development of a rapid assay of ALT activity levels and the construction of molecular models of ALT.

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Figure 1: Structure of telomeres.
Figure 2: Two models of the alternative lengthening of telomeres mechanism.
Figure 3: Alternative copy templates for recombination-mediated synthesis of telomeric DNA.
Figure 4: Closed-state, intermediate-state and uncapped telomeres.

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Acknowledgements

Work in the authors' laboratory was supported by a US National Science Foundation international research fellowship, a project grant from the Cure Cancer Australia Foundation (to A.J.C) and a Cancer Council New South Wales Program Grant (to R.R.R.). Members of the Children's Medical Research Institute are thanked for comments on the manuscript.

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Correspondence to Roger R. Reddel.

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Glossary

End-replication problem

The inability of semi-conservative DNA replication to completely copy the ends of linear DNA molecules. Removal of the RNA primer from the terminal Okazaki fragment on the lagging strand results in incomplete copying of the terminus of that strand, which then provides a shorter template for copying in the next round of DNA synthesis.

DNA-damage response

The coordinated cellular response to DNA damage, including localization of DNA-damage sensing and repair molecules to the site of damage.

Senescence

The permanent removal of a cell from the cell cycle without the loss of viability. Telomere-dependent senescence results from the natural erosion of human telomeres.

Telomerase

The reverse transcriptase that catalytically adds de novo telomeric repeats to the chromosome ends.

Shelterin

The six-subunit protein complex that binds specifically to telomeric DNA and regulates telomere function.

Extrachromosomal telomeric DNA

DNA molecules consisting of telomeric repeats that are not associated with the chromosomes. These fragments can be linear, circular, single-stranded, duplex or more complex structures.

Telomeric circle

A double-stranded circular extrachromosomal DNA molecule containing telomere repeat sequences.

Promyelocytic leukaemia nuclear body

A spherical nuclear structure that is associated with several functions, including DNA repair, senescence, apoptosis, viral defence, proteolysis and stress response, and which is named after one of its constitutive components, promyelocytic leukaemia (PML) protein.

Telomere-loop junction

The DNA structure produced when the single-stranded telomere end is inserted into the duplex telomeric DNA in the formation of a telomere loop.

Telomeric repeat-binding factor 2

A shelterin protein that binds telomeric DNA directly as a homodimer. Its functions include telomere-loop formation, preventing telomere-specific DNA-damage responses and end-to-end chromosome fusions, and inhibiting some forms of telomeric homologous recombination.

Telomere trimming

Telomeres that are overlengthened by telomerase (or presumably by ALT) may undergo rapid shortening events, most likely by telomere-loop junction resolution.

Telomere-loop junction resolution

The processing of a telomere-loop junction by recombination enzymes. This may result in telomere truncation and the production of extrachromosomal telomeric DNA.

Telomere-length maintenance mechanism

Any process that extends telomere length to fully compensate for telomere erosion.

Homologous recombination

The genetic exchange between two DNA molecules of identical or very similar sequences. A strand of DNA from one molecule pairs with the complementary strand of the other molecule and vice versa.

Telomere sister chromatid exchanges

Exchanges of DNA between sister chromatids that are limited to the telomere.

Broken replication forks

When a DNA replication fork encounters a structural barrier it may break, resulting in the termination of coordinated DNA polymerization.

Break-induced replication

Homologous recombination-mediated DNA repair that involves a 3′ overhang from a one-ended DNA break invading a homologous sequence on the end of another chromosome. This primes DNA replication to copy the sequence of the invaded chromosome onto the distal end of the invading chromosome.

Sister telomere loss

When one sister chromatid telomere of a metaphase chromosome end is not replicated owing to errors in DNA polymerization. This results in a telomere signal-free chromosome end.

Protection of telomeres 1

A shelterin subunit that binds single-strand G-rich telomeric DNA. It heterodimerizes with the shelterin subunit TPP1 (also known as ACD) and regulates telomerase access to chromosome ends, protecting the telomere against a telomere-specific DNA-damage response and inhibiting some forms of telomere recombination.

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Cesare, A., Reddel, R. Alternative lengthening of telomeres: models, mechanisms and implications. Nat Rev Genet 11, 319–330 (2010). https://doi.org/10.1038/nrg2763

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