Telomere extension by telomerase and ALT generates variant repeats by mechanistically distinct processes

• Published in: Nucleic acids research 2014-02, Vol.42 (3), p.1733-1746
• Main Authors: Lee, Michael, Hills, Mark, Conomos, Dimitri, Stutz, Michael D, Dagg, Rebecca A, Lau, Loretta M S, Reddel, Roger R, Pickett, Hilda A
• Format: Article
• Language: English
• Subjects: Cell Line; Genetic Variation; Genome Integrity, Repair and; Humans; Repetitive Sequences, Nucleic Acid; Sequence Analysis, DNA; Telomerase - metabolism; Telomere - chemistry; Telomere Homeostasis
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkt1117

Telomeres are terminal repetitive DNA sequences on chromosomes, and are considered to comprise almost exclusively hexameric TTAGGG repeats. We have evaluated telomere sequence content in human cells using whole-genome sequencing followed by telomere read extraction in a panel of mortal cell strains and immortal cell lines. We identified a wide range of telomere variant repeats in human cells, and found evidence that variant repeats are generated by mechanistically distinct processes during telomerase- and ALT-mediated telomere lengthening. Telomerase-mediated telomere extension resulted in biased repeat synthesis of variant repeats that differed from the canonical sequence at positions 1 and 3, but not at positions 2, 4, 5 or 6. This indicates that telomerase is most likely an error-prone reverse transcriptase that misincorporates nucleotides at specific positions on the telomerase RNA template. In contrast, cell lines that use the ALT pathway contained a large range of variant repeats that varied greatly between lines. This is consistent with variant repeats spreading from proximal telomeric regions throughout telomeres in a stochastic manner by recombination-mediated templating of DNA synthesis. The presence of unexpectedly large numbers of variant repeats in cells utilizing either telomere maintenance mechanism suggests a conserved role for variant sequences at human telomeres.