DNA repair in species with extreme lifespan differences

Aging

Volumn 7, Issue 12, 2015, Pages 1171-1184

  MacRae, Sheila L ^a   Croken, Matthew McKnight ^a   Calder, R B ^a   Aliper, Alexander ^b   Milholland, Brandon ^a   White, Ryan R ^a   Zhavoronkov, Alexander ^b   Gladyshev, Vadim N ^d   Seluanov, Andrei ^c   Gorbunova, Vera ^c   Zhang, Zhengdong D ^a   Vijg, Jan ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF ROCHESTER   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Aging; DNA repair; Genome maintenance; Longevity; Naked mole rat; RNA seq; Transcriptome

Indexed keywords

TRANSCRIPTOME;

ANIMAL; DNA REPAIR; GENE EXPRESSION REGULATION; GENETICS; HUMAN; LONGEVITY; MOUSE; PHYSIOLOGY; RAT; SPECIES DIFFERENCE;

ANIMALS; DNA REPAIR; GENE EXPRESSION REGULATION; HUMANS; LONGEVITY; MICE; RATS; SPECIES SPECIFICITY; TRANSCRIPTOME;

EID: 84958155266     PISSN: 19454589     EISSN: None     Source Type: Journal    
DOI: 10.18632/aging.100866     Document Type: Article

References (35)

1. Hoeijmakers JH. DNA damage, aging, and cancer. The New England journal of medicine. 2009; 361:1475-1485.
2. Vijg J and Suh Y. Genome instability and aging. Annual review of physiology. 2013; 75:645-668.
3. Freitas AA and de Magalhaes JP. A review and appraisal of the DNA damage theory of ageing. Mutat Res. 2011; 728:12-22.
4. Hart RW and Setlow RB. Correlation between deoxyribonucleic acid excision-repair and life-span in a number of mammalian species. Proc Natl Acad Sci U S A. 1974; 71:2169-2173.
5. Hanawalt PC. Revisiting the rodent repairadox. Environ Mol Mutagen. 2001; 38:89-96.
6. Gorbunova V, Seluanov A, Zhang ZD, Gladyshev VN and Vijg J. Comparative genetics of longevity and cancer: insights from long-lived rodents. Nat Rev Genet. 2014; 15:531-540.
7. MacRae SL, Zhang Q, Lemetre C, Seim I, Calder RB, Hoeijmakers J, Suh Y, Gladyshev VN, Seluanov A, Gorbunova V, Vijg J and Zhang ZD. Comparative analysis of genome maintenance genes in naked mole rat, mouse, and human. Aging Cell. 2015; 14:288-291.
8. Christmann M and Kaina B. Transcriptional regulation of human DNA repair genes following genotoxic stress: trigger mechanisms, inducible responses and genotoxic adaptation. Nucleic Acids Res. 2013; 41:8403-8420.
9. Roschke AV, Glebov OK, Lababidi S, Gehlhaus KS, Weinstein JN and Kirsch IR. Chromosomal instability is associated with higher expression of genes implicated in epithelial-mesenchymal transition, cancer invasiveness, and metastasis and with lower expression of genes involved in cell cycle checkpoints, DNA repair, and chromatin maintenance. Neoplasia. 2008; 10:1222-1230.
10. Cichoz-Lach H and Michalak A. Oxidative stress as a crucial factor in liver diseases. World J Gastroentero. 2014; 20:8082-8091.
11. Keane M, Craig T, Alfoldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V, Di Palma F, Lindblad-Toh K, Church GM and de Magalhaes JP. The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations. Bioinformatics. 2014; 30:3558-3560.
12. Bullard JH, Purdom E, Hansen KD and Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics. 2010; 11:94.
13. Wood RD, Mitchell M and Lindahl T. Human DNA repair genes, 2005. Mutat Res. 2005; 577:275-283.
14. Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K and Bujnicki JM. REPAIRtoire-a database of DNA repair pathways. Nucleic Acids Res. 2011; 39:D788-792.
15. Smith ML and Seo YR. p53 regulation of DNA excision repair pathways. Mutagenesis. 2002; 17:149-156.
16. Christmann M, Tomicic MT, Roos WP and Kaina B. Mechanisms of human DNA repair: an update. Toxicology. 2003; 193:3-34.
17. Buzdin AA, Zhavoronkov AA, Korzinkin MB, Venkova LS, Zenin AA, Smirnov PY and Borisov NM. Oncofinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data. Front Genet. 2014; 5:55.
18. Tarazona S, Furio-Tari P, Turra D, Pietro AD, Nueda MJ, Ferrer A and Conesa A. Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package. Nucleic Acids Res. 2015; 21:e140.
19. Eden E, Navon R, Steinfeld I, Lipson D and Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics. 2009; 10:48.
20. Supek F, Bosnjak M, Skunca N and Smuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE. 2011; 6:e21800.
21. Prall WC, Czibere A, Jager M, Spentzos D, Libermann TA, Gattermann N, Haas R and Aivado M. Age-related transcription levels of KU70, MGST1 and BIK in CD34+ hematopoietic stem and progenitor cells. Mech Ageing Dev. 2007; 128:503-510.
22. Ju YJ, Lee KH, Park JE, Yi YS, Yun MY, Ham YH, Kim TJ, Choi HM, Han GJ, Lee JH, Lee J, Han JS, Lee KM, et al. Decreased expression of DNA repair proteins Ku70 and Mre11 is associated with aging and may contribute to the cellular senescence. Exp Mol Med. 2006; 38:686-693.
23. Zucca E, Bertoletti F, Wimmer U, Ferrari E, Mazzini G, Khoronenkova S, Grosse N, van Loon B, Dianov G, Hubscher U and Maga G. Silencing of human DNA polymerase lambda causes replication stress and is synthetically lethal with an impaired S phase checkpoint. Nucleic Acids Res. 2013; 41:229-241.
24. Haracska L, Prakash L and Prakash S. Role of human DNA polymerase kappa as an extender in translesion synthesis. Proceedings of the National Academy of Sciences of the United States of America. 2002; 99:16000-16005.
25. Mao Z, Hine C, Tian X, Van Meter M, Au M, Vaidya A, Seluanov A and Gorbunova V. SIRT6 promotes DNA repair under stress by activating PARP1. Science. 2011; 332:1443-1446.
26. Christmann M and Kaina B. Transcriptional regulation of human DNA repair genes following genotoxic stress: trigger mechanisms, inducible responses and genotoxic adaptation. Nucleic Acids Research. 2013; 41:8403-8420.
27. Dollé ME, Giese H, Hopkins CL, Martus HJ, Hausdorff JM and Vijg J. Rapid accumulation of genome rearrangements in liver but not in brain of old mice. Nature Genetics. 1997; 17:431-434.
28. White RR, Milholland B, de Bruin A, Curran S, Laberge RM, van Steeg H, Campisi J, Maslov AY and Vijg J. Controlled induction of DNA double-strand breaks in the mouse liver induces features of tissue ageing. Nat Commun. 2015; 6:6790.
29. Azpurua J, Ke Z, Chen IX, Zhang Q, Ermolenko DN, Zhang ZD, Gorbunova V and Seluanov A. Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage. Proc Natl Acad Sci U S A. 2013; 110:17350-17355.
30. White RR, Milholland B, MacRae SL, Lin M, Zheng D and Vijg J. Comprehensive transcriptional landscape of aging mouse liver. BMC Genomics. 2015; 16:899.
31. Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR and Snyder MP. Comparison of the transcriptional landscapes between human and mouse tissues. Proc Natl Acad Sci U S A. 2014; 111:17224-17229.
32. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM and Haussler D. The human genome browser at UCSC. Genome Res. 2002; 12:996-1006.
33. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M and Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29:15-21.
34. Anders S, Pyl PT and Huber W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015; 31:166-169.
35. R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2013.