Characterization of nucleotide misincorporation patterns in the Iceman's mitochondrial DNA

PLoS ONE

Volumn 5, Issue 1, 2010, Pages

  Olivieri, Cristina ^a   Ermini, Luca ^b   Rizzi, Ermanno ^c   Corti, Giorgio ^c   Bonnal, Raoul ^c   Luciani, Stefania ^a   Marota, Isolina ^a   De Bellis, Gianluca ^c   Rollo, Franco ^a  

^a UNIVERSITY OF CAMERINO   (Italy)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

^c CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA; NUCLEOTIDE;

ARTICLE; DNA DEGRADATION; DNA SEQUENCE; FOSSIL HUMAN; HUMAN; NUCLEOTIDE MISCORPORATION; POLYMERASE CHAIN REACTION; PYROSEQUENCING; FOSSIL; FREEZING; GENETICS; METABOLISM; PALEONTOLOGY;

DNA, MITOCHONDRIAL; FOSSILS; FREEZING; HUMANS; NUCLEOTIDES; PALEONTOLOGY;

EID: 77649125287     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008629     Document Type: Article

References (42)

1. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362: 709-715.
2. Eglinton G, Logan GA (1991) Molecular preservation. Philos Trans R Soc Lond 333: 315-327.
3. Friedberg EC, Walker GC, Siede W (1995) DNA repair and mutagenesis. Washington, DC: ASM Press.
4. Di Bernardo G, Del Gaudio S, Cammarota M, Galderisi U, Cascino A, et al. (2002) Enzymatic repair of selected cross-linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains. Nucleic Acids Res 30: e16.
5. Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, et al. (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38: 645-79.
6. Poinar HN, Hofreiter M, Spaulding WG, Martin PS, Stankiewicz BA, et al. (1998) Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281: 402-406.
7. Pääbo S (1989) Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci USA 86: 1939-1943.
8. Handt O, Richards M, Tromsdorff M, Kilger C, Simanainen J, et al. (1994) Molecular genetic analyses of the Tyrolean Ice Man. Science 264: 1775-1778.
9. Höss M, Jaruga P, Zastawny T, Dizdaroglu M, Pääbo S (1996) DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res 24: 1304-1307.
10. Hofreiter M, Serre D, Poinar HN, Kuch M, Pääbo S (2001) Ancient DNA. Nature Rev Genet 2: 353-360.
11. 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.
12. Gilbert MTP, Hansen AJ, Willerslev E, Rudbeck L, Barnes I, et al. (2003) Distribution patterns of post mortem damage in human mitochondrial DNA. Am J Hum Genet 72: 32-47.
13. Gilbert MTP, Hansen AJ, Willerslev E, Rudbeck L, Barnes I, et al. (2003) Characterization of genetic miscoding lesions caused by postmortem damage. Am J Hum Genet 72: 48-61.
14. Banerjeea M, Terence A (2004) BrownNon-random DNA damage resulting from heat treatment: implications for sequence analysis of ancient DNA. J Archaeol Sci 31: 59-63.
15. Willerslev E, Hansen AJ, Rønn R, Brand TB, Barnes I, et al. (2004) Long-term persistence of bacterial DNA. Curr Biol 14: R9-10.
16. Gilbert MTP, Hansen AJ (2005) Post mortem damage in aDNA: implications and assessing aDNA quality. In: G. Dorado, Editor, Molecular Markers, PCR, Bioinformatics and Ancient DNA - Technology, Troubleshooting And Applications, Science Publishers.
17. Eckert KA, Kunkel TA (1990) The fidelity of DNA polymerase used in the polymerase chain reaction. In: McPherson MJ, Quirke P, Taylor GR, eds. PCR: a practical approach. Oxford, England: IRL Press, Oxford University Press. pp 225-244.
18. Binladen J, Wiuf C, Gilbert MTP, Bunce M, Larson G, et al. (2006) Comparing miscoding lesion damage in mitochondrial and nuclear ancient DNA. Genetics 172: 733-741.
19. Stiller M, Green RE, Ronan M, Simons JF, Du L, et al. (2006) Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc Natl Acad Sci USA 103: 13578-13584.
20. Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, et al. (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci USA 104: 14616-14621.
21. Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, et al. (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.
22. Gilbert MTP, Binladen J, Miller W, Wiuf C, Willerslev E, et al. (2007) Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res 35: 1-10.
23. Lamers R, Hayter S, Matheson CD (2009) Postmortem Miscoding Lesions in Sequence Analysis of Human AncientMitochondrial DNA. J Mol Evol 68: 40-55.
24. Ermini L, Olivieri C, Rizzi E, Corti G, Bonnal R, et al. (2008) The Complete Mitochondrial Genome Sequence of the Tyrolean Iceman. Curr Biol 18: 1687-1693.
25. Spindler K (1994) The Man in the Ice. London: Weidenfeld & Nicholson.
26. Margulies M, Egholm M, Altan WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
27. Ubaldi M, Luciani S, Marota I, Fornaciari G, Cano RJ, et al. (1998) Sequence analysis of bacterial DNA in the colon of an Andean mummy. Am J Phys Anthropol 107: 285-295.
28. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, et al. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23: 147.
29. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
30. Frey JE, Frey B (2004) Origin of intra-individual variation in PCR-amplified mitochondrial cytochrome oxidase I of Thrips tabaci (Thysanoptera: Thripidae): mitochondrial heteroplasmy or nuclear integration? Hereditas 140: 92-98.
31. Marota I, Basile C, Ubaldi M, Rollo F (2002) DNA decay rate in papyri and human remains from Egyptian archaeological sites. Am J Phys Anthropol 117: 310-318.
32. Gilbert MT, Barnes I, Collins MJ, Smith C, Eklund J, et al. (2005) Long-term survival of ancient DNA in Egypt: response to Zink and Nerlich. Am J Phys Anthropol 128: 110-114.
33. Noonan JP, Hofreiter M, Smith D, Priest JR, Rohland N, et al. (2005) Genomic sequencing of Pleistocene cave bears. Science 309: 597-599.
34. Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RD, et al. (2006) Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311: 392-394.
35. Brown TA, Brown KA (1992) Ancient DNA and the archaeologist. Antiquity 66: 10-23.
36. Handt O, Krings M, Ward RH, Pääbo S (1996) The retrieval of ancient human DNA sequences. Am J Hum Genet 59: 368-376.
37. Cooper A, Poinar H (2000) Ancient DNA: Do it right or not at all. Science 289: 1139.
38. Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, et al. (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38: 645-79.
39. Gilbert MTP, Bandelt HJ, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends Ecol Evol 20: 541-544.
40. Willerslev E, Cooper A (2005) Ancient DNA. Proc Biol Sci 272: 3-16.
41. Sampietro ML, Gilbert MT, Lao O, Caramelli D, Lari M, et al. (2006) Tracking down human contamination in ancient human teeth. Mol Biol Evol 23: 1801-1807.
42. Helgason A, Pálsson S, Lalueza-Fox C, Ghosh S, Sigurdardóttir S, et al. (2007) A statistical approach to identify ancient template DNA. J Mol Evol 65: 92-102.