LORD-Q: A long-run real-time PCR-based DNA-damage quantification method for nuclear and mitochondrial genome analysis

Nucleic Acids Research

Volumn 42, Issue 6, 2014, Pages

  Lehle, Simon ^a   Hildebrand, Dominic G ^a   Merz, Britta ^a   Malak, Peter N ^a   Becker, Michael S ^b   Schmezer, Peter ^b   Essmann, Frank ^a   Schulze Osthoff, Klaus ^a,b   Rothfuss, Oliver ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS; CELLS, CULTURED; COMET ASSAY; DNA DAMAGE; DNA, MITOCHONDRIAL; GENOME, MITOCHONDRIAL; HUMANS; JURKAT CELLS; REAL-TIME POLYMERASE CHAIN REACTION;

EID: 84899002971     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1349     Document Type: Article

References (40)

1. Wagener, S., Volker, T., De Spirt, S., Ernst, H. and Stahl, W. (2012) 3,3'-Dihydroxyisorenieratene and isorenieratene prevent UVinduced DNA damage in human skin fibroblasts. Free Rad. Biol. Med., 53, 457-463.
2. Balajee, A. S., May, A. and Bohr, V. A. (1999) DNA repair of pyrimidine dimers and 6-4 photoproducts in the ribosomal DN A. Nucleic Acids Res., 27, 2511-2520.
3. Hewitt, G., Jurk, D., Marques, F. D., Correia-Melo, C., Hardy, T., Gackowska, A., Anderson, R., Taschuk, M., Mann, J. and Passos, J. F. (2012) Telomeres are favoured targets of a persistent DNA damage response in ageing and stress-induced senescence. Nat. Commun., 3, 708.
4. Seo, J., Kim, S. C., Lee, H. S., Kim, J. K., Shon, H. J., Salleh, N. L., Desai, K. V., Lee, J. H., Kang, E. S., Kim, J. S. et al. (2012) Genomewide profiles of H2AX and gamma-H2AX differentiate endogenous and exogenous DNA damage hotspots in human cells. Nucleic Acids Res., 40, 5965-5974.
5. Santos, J. H., Meyer, J. N., Mandavilli, B. S. and Van Houten, B. (2006) Quantitative PCR-based measurement of nuclear and mitochondrial DNA damage and repair in mammalian cells. Methods Mol. Biol., 314, 183-199.
6. Furda, A. M., Bess, A. S., Meyer, J. N. and Van Houten, B. (2012) Analysis of DNA damage and repair in nuclear and mitochondrial DNA of animal cells using quantitative PC R. Methods Mol. Biol., 920, 111-132.
7. Hunter, S. E., Jung, D., Di Giulio, R. T. and Meyer, J. N. (2010) The QPCR assay for analysis of mitochondrial DNA damage, repair, and relative copy number. Methods, 51, 444-451.
8. Rothfuss, O., Gasser, T. and Patenge, N. (2010) Analysis of differential DNA damage in the mitochondrial genome employing a semi-long run real-time PCR approach. Nucleic Acids Res., 38, e24.
9. Gudnason, H., Dufva, M., Bang, D. D. and Wolff, A. (2007) Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature. Nucleic Acids Res., 35, e127.
10. Edwards, J. G. (2009) Quantification of mitochondrial DNA (mtDNA) damage and error rates by real-time QPC R. Mitochondrion, 9, 31-35.
11. Bustin, S. A., Benes, V., Garson, J. A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M. W., Shipley, G. L. et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem., 55, 611-622.
12. Mourier, T., Hansen, A. J., Willerslev, E. and Arctander, P. (2001) The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Mol. Biol. Evol., 18, 1833-1837.
13. Greve, B., Bolling, T., Amler, S., Rossler, U., Gomolka, M., Mayer, C., Popanda, O., Dreffke, K., Rickinger, A., Fritz, E. et al. (2012) Evaluation of different biomarkers to predict individual radiosensitivity in an inter-laboratory comparison -lessons for future studies. PLoS One, 7, e47185.
14. Schmezer, P., Rajaee-Behbahani, N., Risch, A., Thiel, S., Rittgen, W., Drings, P., Dienemann, H., Kayser, K. W., Schulz, V. and Bartsch, H. (2001) Rapid screening assay for mutagen sensitivity and DNA repair capacity in human peripheral blood lymphocytes. Mutagenesis, 16, 25-30.
15. Park, I. H. and Daley, G. Q. (2009) Human iPS cell derivation/ reprogramming. Curr. Protoc. Stem Cell Biol., Chapter 4, Unit 4 A.1, doi:10.1002/9780470151808.sc04a01s8.
16. Rothfuss, O., Fischer, H., Hasegawa, T., Maisel, M., Leitner, P., Miesel, F., Sharma, M., Bornemann, A., Berg, D., Gasser, T. et al. (2009) Parkin protects mitochondrial genome integrity and supports mitochondrial DNA repair. Hum. Mol. Genet., 18, 3832-3850.
17. Livak, K. J. and Schmittgen, T. D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods, 25, 402-408.
18. Horakova, H., Polakovicova, I., Shaik, G. M., Eitler, J., Bugajev, V., Draberova, L. and Draber, P. (2011) 1,2-propanediol-trehalose mixture as a potent quantitative real-time PCR enhancer. BMC Biotechnol., 11, 41.
19. Oliver, R., Bjoertomt, O., Greenwood, R. and Rothwell, J. (2008) 'Noisy patients'-can signal detection theory help? Nat. Clin. Pract. Neurol., 4, 306-316.
20. Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P. et al. (2011) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature, 473, 394-397.
21. Booth, M. J., Branco, M. R., Ficz, G., Oxley, D., Krueger, F., Reik, W. and Balasubramanian, S. (2012) Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution. Science, 336, 215-228.
22. Song, C. X., Clark, T. A., Lu, X. Y., Kislyuk, A., Dai, Q., Turner, S. W., He, C. and Korlach, J. (2012) Sensitive and specific singlemolecule sequencing of 5-hydroxymethylcytosine. Nat. Methods, 9, 75-77.
23. Broyde, S. and Patel, D. J. (2010) DNA repair: How to accurately bypass damage. Nature, 465, 1023-1024.
24. McKinnon, P. J. (2012) ATM and the molecular pathogenesis of ataxia telangiectasia. Annu. Rev. Pathol., 7, 303-321.
25. Zhou, W., Otto, E. A., Cluckey, A., Airik, R., Hurd, T. W., Chaki, M., Diaz, K., Lach, F. P., Bennett, G. R., Gee, H. Y. et al. (2012) FAN1 mutations cause karyomegalic interstitial nephritis, linking chronic kidney failure to defective DNA damage repair. Nat. Genet., 44, 910-915.
26. Devine, M. J., Plun-Favreau, H. and Wood, N. W. (2011) Parkinson's disease and cancer: two wars, one front. Nat. Rev. Cancer, 11, 812-823.
27. Lord, C. J. and Ashworth, A. (2012) The DNA damage response and cancer therapy. Nature, 481, 287-294.
28. Luo, L. Z., Gopalakrishna-Pillai, S., Nay, S. L., Park, S. W., Bates, S. E., Zeng, X., Iverson, L. E. and O'Connor, T. R. (2012) DNA repair in human pluripotent stem cells is distinct from that in non-pluripotent human cells. PLoS One, 7, e30541.
29. Maynard, S., Swistowska, A. M., Lee, J. W., Liu, Y., Liu, S. T., Da Cruz, A. B., Rao, M., de Souza-Pinto, N. C., Zeng, X. and Bohr, V. A. (2008) Human embryonic stem cells have enhanced repair of multiple forms of DNA damage. Stem Cells, 26, 2266-2274.
30. Momcilovic, O., Knobloch, L., Fornsaglio, J., Varum, S., Easley, C. and Schatten, G. (2010) DNA damage responses in human induced pluripotent stem cells and embryonic stem cells. PLoS One, 5, e13410.
31. Taylor, R. W. and Turnbull, D. M. (2005) Mitochondrial DNA mutations in human disease. Nat. Rev. Genet., 6, 389-402.
32. Mabeta, P., Dippenaar, N. and Shelver, G. (2012) A validated HPLC method for the simultaneous determination of bleomycin A2 and B2 in human plasma. Int. J. Pharm. Biomed. Res., 3, 191-194.
33. Dumitru, R., Gama, V., Fagan, B. M., Bower, J. J., Swahari, V., Pevny, L. H. and Deshmukh, M. (2012) Human embryonic stem cells have constitutively active Bax at the Golgi and are primed to undergo rapid apoptosis. Mol. Cell, 46, 573-583.
34. Szewczyk, A. and Wojtczak, L. (2002) Mitochondria as a pharmacological target. Pharmacol. Rev., 54, 101-127.
35. Lim, L. O. and Neims, A. H. (1987) Mitochondrial DNA damage by bleomycin. Biochem. Pharmacol., 36, 2769-2774.
36. Brar, S. S., Meyer, J. N., Bortner, C. D., Van Houten, B. and Martin, W. J. 2nd (2012) Mitochondrial DNA-depleted A549 cells are resistant to bleomycin. Am. J. Physiol. Lung Cell. Mol. Physiol., 303, L413-L424.
37. Champoux, J. J. (2001) DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem., 70, 369-413.
38. Rass, K. and Reichrath, J. (2008) UV damage and DNA repair in malignant melanoma and nonmelanoma skin cancer. Adv. Exp. Med. Biol., 624, 162-178.
39. Hackett, J. A., Sengupta, R., Zylicz, J. J., Murakami, K., Lee, C., Down, T. A. and Surani, M. A. (2012) Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine. Science, 339, 448-452.
40. Hackett, J. A., Reddington, J. P., Nestor, C. E., Dunican, D. S., Branco, M. R., Reichmann, J., Reik, W., Surani, M. A., Adams, I. R. and Meehan, R. R. (2012) Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline. Development, 139, 3623-3632.