Ancient DNA damage

Cold Spring Harbor Perspectives in Biology

Volumn 5, Issue 7, 2013, Pages

  Dabney, Jesse ^a   Meyer, Matthias ^a   Pääbo, Svante ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CHEMISTRY; DEAMINATION; DNA DAMAGE; DNA FRAGMENTATION; DNA SEQUENCE; TIME;

DEAMINATION; DNA; DNA DAMAGE; DNA FRAGMENTATION; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

EID: 84879757867     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a012567     Document Type: Article

References (34)

1. Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego JA, Gilbert MTP, Willerslev E, et al. 2012. The half-life of DNA in bone: Measuring decay kinetics in 158 dated fossils. Proc R Soc B doi: 10.1098/rspb.2012.1745.
2. Binladen J, Willerslev E. 2010. Why study ancient DNA damage? J Nordic Archaeol Sci 14: 11-14.
3. Binladen J, Wiuf C, Gilbert MTP, Bunce M, Barnett R, Larson G, Greenwood AD, Haile J, HoSYW, Hansen AJ, et al. 2006. Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics 172: 733-741.
4. Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X, et al. 2008. The potential and challenges of nanopore sequencing. Nat Biotechnol 26: 1146-1153.
5. Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, et al. 2007. Patterns of damage in genomicDNA sequences from a Neandertal. Proc Natl Acad Sci 104: 14616-14621.
6. Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Pääbo S. 2010. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res 38: e87.
7. Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, Cooper A. 2007. Novel high-resolution characterization of ancient DNA reveals C. U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res 35: 5717-5728.
8. DeSalle R, Gatesy J, Wheeler W, Grimaldi D. 1992. DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications. Science (New York, NY) 257: 1933-1936.
9. Gilbert MTP, Willerslev E, Hansen AJ, Barnes I, Rudbeck L, Lynnerup N, Cooper A. 2003. Distribution patterns of postmortem damage in human mitochondrial DNA. Am J Hum Genet 72: 32-47.
10. Gilbert MTP, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster SC. 2007. Recharacterization of ancient DNA miscoding lesions: Insights in the era of sequencing-by-synthesis. Nucleic Acids Res 35: 1-10.
11. Golenberg EM, Giannasi DE, Clegg MT, Smiley CJ, Durbin M, Henderson D, Zurawski G. 1990. Chloroplast DNA sequence from a miocene Magnolia species. Nature 344: 656-658.
12. Hansen AJ, Willerslev E, Wiuf C, Mourier T, Arctander P. 2001. Statistical evidence for miscoding lesions in ancient DNA templates. Mol Biol Evol 18: 262-265.
13. Hansen AJ, Mitchell DL, Wiuf C, Paniker L, Brand TB, Binladen J, Gilichinsky D A, Rønn R, Willerslev E. 2006. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics 173: 1175-1179.
14. Heyn P, Stenzel U, Briggs AW, Kircher M, Hofreiter M, Meyer M. 2010. Road blocks on paleogenomes-polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA. Nucleic Acids Res 38: e161.
15. Hofreiter M, Jaenicke V, Serre D, von Haeseler A, Pääbo S. 2001. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res 29: 4793-4799.
16. Höss M, Jaruga P, Zastawny TH, Dizdaroglu M, Pääbo S. 1996. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res 24: 1304-1307.
17. Jones AS, Mian AM, Walker RTJ. 1968. Chem Soc C 2042-2044.
18. Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, Pääbo S. 2010. A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol 20: 231-236.
19. Lindahl T. 1993. Instability and decay of the primary structure of DNA. Nature 362: 709-715.
20. Lindahl T, Andersson A. 1972. Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry 11: 3618-3623.
21. Lindahl T, Nyberg B. 1972. Rate of depurination of native deoxyribonucleic acid. Biochemistry 11: 3610-3618.
22. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437: 376-380.
23. Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, De Filippo C, et al. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science (New York, NY) 338: 222-226.
24. Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, et al. 2011. True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res 21: 1705-1719.
25. Overballe-Petersen S, Orlando L, Willerslev E. 2012. Nextgeneration sequencing offers new insights intoDNA degradation. Trends Biotechnol 30: 364-368.
26. Pääbo S. 1989. Ancient DNA: Extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci 86: 1939-1943.
27. Pääbo S, Wilson AC. 1991. Miocene DNA sequences-A dream come true? Curr Biol 1: 45-46.
28. Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M. 2004. Genetic analyses from ancient DNA. Annu Rev Genet 38: 645-679.
29. Poinar HN, Hofreiter M, Spaulding GW, Martin PS, Stankiewicz BA, Bland H, Evershed RP, Possnert G, Pääbo S. 1998. Molecular coproscopy: Dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281: 402-406.
30. Rohland N, Hofreiter M. 2007. Comparison and optimization of ancient DNA extraction. BioTechniques 42: 343-352.
31. Sawyer S, Krause J, Guschanski K, Savolainen V, Pääbo S. 2012. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PloS ONE 7: e34131.
32. Stiller M, Green RE, Ronan M, Simons JF, Du L, He W, Egholm M, Rothberg JM, Keates SG, Keats SG, et al. 2006. Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc Natl Acad Sci 103: 13578-13584.
33. Willerslev E, Cappellini E, Boomsma W, Nielsen R, Hebsgaard MB, Brand TB, Hofreiter M, Bunce M, Poinar HN, Dahl-Jensen D, et al. 2007. Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science (New York, NY) 317: 111-114.
34. Woodward SR, Weyand NJ, Bunnell M. 1994. DNA sequence from Cretaceous period bone fragments. Science (New York, NY) 266: 1229-1232.