Telomere maintenance through recruitment of internal genomic regions

Nature Communications

Volumn 6, Issue , 2015, Pages

  Seo, Beomseok ^a   Kim, Chuna ^a   Hills, Mark ^b   Sung, Sanghyun ^a   Kim, Hyesook ^a   Kim, Eunkyeong ^a   Lim, Daisy S ^a   Oh, Hyun Seok ^a   Choi, Rachael Mi Jung ^a   Chun, Jongsik ^a   Shim, Jaegal ^c   Lee, Junho ^a  

^a Seoul National University   (South Korea)

^b BRITISH COLUMBIA CANCER AGENCY   (Canada)

^c National Cancer Center   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; CAENORHABDITIS ELEGANS PROTEIN; DNA; TELOMERASE;

ANCESTRY; CELLS AND CELL COMPONENTS; CHROMOSOME; DNA; GENETIC ANALYSIS; GENOMICS;

ALTERNATIVE LENGTHENING OF TELOMERE; ARTICLE; CAENORHABDITIS ELEGANS; CHROMOSOME; CONTROLLED STUDY; DNA FLANKING REGION; DOUBLE STRANDED DNA BREAK; EMBRYO; FLUORESCENCE IN SITU HYBRIDIZATION; NONHUMAN; SINGLE NUCLEOTIDE POLYMORPHISM; TELOMERE; TELOMERE HOMEOSTASIS; TEMPLATE FOR ALTERNATIVE LENGTHENING OF TELOMERE REGION; ANIMAL; GENETIC RECOMBINATION; GENETICS; SOUTHERN BLOTTING; TRANSGENIC ANIMAL;

CAENORHABDITIS ELEGANS;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; BLOTTING, SOUTHERN; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; DNA; IN SITU HYBRIDIZATION, FLUORESCENCE; RECOMBINATION, GENETIC; TELOMERASE; TELOMERE HOMEOSTASIS;

EID: 84942016751     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms9189     Document Type: Article

References (34)

1. Olovnikov, A. M. A theory of marginotomy: the incomplete copying of template margin in enzymic synthesis of polynucleotides and biological significance of the phenomenon. J. Theor. Biol. 41, 181-190 (1973).
2. Shay, J. & Bacchetti, S. A survey of telomerase activity in human cancer. Eur. J. Cancer 33, 787-791 (1997).
3. Cesare, A. J. & Reddel, R. R. Alternative lengthening of telomeres: models, mechanisms and implications. Nat. Rev. Genet. 11, 319-330 (2010).
4. Heaphy, C. M. et al. Altered telomeres in tumors with ATRX and DAXX mutations. Science 333, 425-425 (2011).
5. Lovejoy, C. A. et al. Loss of ATRX, genome instability, and an altered DNA damage response are hallmarks of the alternative lengthening of telomeres pathway. PLoS Genet. 8, e1002772 (2012).
6. Conomos, D., Reddel, R. R. & Pickett, H. A. NuRD-ZNF827 recruitment to telomeres creates a molecular scaffold for homologous recombination. Nat. Struct. Mol. Biol. 21, 760-770 (2014).
7. Meier, B. et al. trt-1 is the Caenorhabditis elegans catalytic subunit of telomerase. PLoS Genet. 2, e18 (2006).
8. Andersen, E. C. et al. Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nat. Genet. 44, 285-290 (2012).
9. Cheng, C., Shtessel, L., Brady, M. M. & Ahmed, S. Caenorhabditis elegans POT-2 telomere protein represses a mode of alternative lengthening of telomeres with normal telomere lengths. Proc. Natl Acad. Sci. USA 109, 7805-7810 (2012).
10. Greiss, S., Schumacher, B., Grandien, K., Rothblatt, J. & Gartner, A. Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 family. BMC Genomics 9, 334 (2008).
11. Cesare, A. J. et al. Spontaneous occurrence of telomeric DNA damage response in the absence of chromosome fusions. Nat. Struct. Mol. Biol. 16, 1244-1251 (2009).
12. 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).
13. Dunham, M. A., Neumann, A. A., Fasching, C. L. & Reddel, R. R. Telomere maintenance by recombination in human cells. Nat. Genet. 26, 447-450 (2000).
14. Royle, N. J., Baird, D. M. & Jeffreys, A. J. A subterminal satellite located adjacent to telomseres in chimpanzees is absent from the human genome. Nat. Genet. 6, 52-56 (1994).
15. Baird, D. & Royle, N. 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).
16. Henson, J. D. et al. DNA C-circles are specific and quantifiable markers of alternative-lengthening-of-telomeres activity. Nat. Biotechnol. 27, 1181-1185 (2009).
17. Bailey, S. M., Brenneman, M. A. & Goodwin, E. H. Frequent recombination in telomeric DNA may extend the proliferative life of telomerase-negative cells. Nucleic Acids Res. 32, 3743-3751 (2004).
18. Conomos, D. et al. Variant repeats are interspersed throughout the telomeres and recruit nuclear receptors in ALT cells. J. Cell Biol. 199, 893-906 (2012).
19. Lee, M. et al. Telomere extension by telomerase and ALT generates variant repeats by mechanistically distinct processes. Nucleic Acids Res. 42, 1733-1746 (2014).
20. Fasching, C. L., Bower, K. & Reddel, R. R. Telomerase-independent telomere length maintenance in the absence of alternative lengthening of telomeres-associated promyelocytic leukemia bodies. Cancer Res. 65, 2722-2729 (2005).
21. Marciniak, R. A. et al. A novel telomere structure in a human alternative lengthening of telomeres cell line. Cancer Res. 65, 2730-2737 (2005).
22. Brenner, S. The genetics of Caenorhabditis elegans. Genetics 77, 71-94 (1974).
23. Shtessel, L. et al. Caenorhabditis elegans POT-1 and POT-2 repress telomere maintenance pathways. G3 (Bethesda) 3, 305-313 (2013).
24. Lackner, D. H., Raices, M., Maruyama, H., Haggblom, C. & Karlseder, J. Organismal propagation in the absence of a functional telomerase pathway in Caenorhabditis elegans. EMBO J. 31, 2024-2033 (2012).
25. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).
26. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
27. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
28. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
29. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
30. Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
31. Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562-578 (2012).
32. Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
33. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
34. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).