Characterization of genetic miscoding lesions caused by postmortem damage

American Journal of Human Genetics

Volumn 72, Issue 1, 2003, Pages 48-61

  Gilbert, M Thomas P ^a   Hansen, Anders J ^b   Willerslev, Eske ^b   Rudbeck, Lars ^b   Barnes, Ian ^a,c   Lynnerup, Niels ^b   Cooper, Alan ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; COMPLEMENTARY DNA; CYTOSINE; GUANINE; HYPOXANTHINE; MITOCHONDRIAL DNA; THYMINE; URACIL;

ARTICLE; CADAVER; CONTROLLED STUDY; DEAMINATION; DNA DETERMINATION; DNA SEQUENCE; DNA STRAND; DNA STRAND BREAKAGE; GENETIC CODE; HUMAN; MITOCHONDRIAL GENETICS; MOLECULAR CLONING; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

EID: 0037219671     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/345379     Document Type: Article

References (39)

1. Anderson S, Bankier A, Arrell B, de Bruijn M, Coulson A, Drouin J, Eperon I, Nierlich D, Roe B, Sanger F, Schreier P, Smith A, Staden R, Young I (1981) Sequence and organisation of the human mitochondrial genome. Nature 290:457-465
2. Ånensen H, Provan F, Lian A, Reinertsen S-H, Ueno Y, Matsuda A, Seeberg E, Bjelland S (2001) Mutations induced by 5-formyl-2′-deoxyuridine in Escherichia coli include base substitutions that can arise from mispairs of 5-formyluracil with guanine, cytosine and thymine. Murat Res 476:99-107
3. Bada J, Wang X, Hamilton H (1999) Preservation of key biomolecules in the fossil record: Current knowledge and future challenges. Philos Trans R Soc Lond B Biol Sci 354:77-87
4. Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A (2002) Dynamics of Pleistocene population extinctions in Beringian brown bears. Science 295:2267-2270
5. Burger J, Hummel S, Herrmann B, Henke W (1999) DNA preservation: A microsatellite-DNA study on ancient skeletal remains. Electophoresis 20:1722-1728
6. Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J, Ward R (2001) Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409:704-707
7. Di Benedetto G, Nasidze IS, Stenico M, Nigro L, Krings M, Lanziger M, Vigilant L, Stoneking M, Pääbo S, Barbujani G (2000) Mitochondrial DNA sequences in prehistoric human remains from the Alps. Eur J Hum Genet 8:669-677
8. Drancourt M, Aboudharam G, Signoli M, Dutour O, Raoult D (1998) Detection of 400-year-old Yersinia pestis DNA in human dental pulp: An approach to the diagnosis of ancient septicemia. Proc Natl Acad Sci USA 95:12637-12640
9. Dunning AM, Talmud P, Humphries SE (1988) Errors in the polymerase chain reaction. Nucleic Acids Res 16:10393
10. 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 University Press, Oxford, UK, pp 225-244
11. Fattorini P, Ciofuli R, Cossutta F, Giulianini P, Edomi P, Furlanut M, Previdere C (1999) Fidelity of polymerase chain reaction-direct sequencing analysis of damaged forensic samples. Electrophoresis 20:3349-3357
12. Fujikawa K, Kamiya H, Kasai H (1998) The mutations induced by oxidatively damaged nucleotides, 5-formyl-dUTP and 5-hydroxy-dCTP, in Escherichia coli. Nucleic Acids Res 26:4582-4587
13. 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 (in this issue)
14. Handt O, Krings M, Ward R, Pääbo S (1996) The retrieval of ancient human DNA sequences. Am J Hum Genet 59:368-376
15. Hansen A, Willerslev E, Wiuf C, Mourier T, Arctander P (2001) Statistical evidence for miscoding lesions in ancient DNA templates. Mol Biol Evol 18:262-265
16. Hillis DM, Mable BK, Larson A, Davis SK, Zimmer EA (1996) Nucleic acids. IV. Sequencing and cloning. In: Hillis DM, Moritz C, Mable BK (eds) Molecular Systematics. Sinauer Associates, Sunderland, MA, pp 321-381
17. 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 29:4693-4799
18. Höss M, Jaruga P, Zastawny T, Dizdaroglu M, Pääbo S (1996) DNA damage and DNA sequence retrieval from ancient tissue. Nucleic Acids Res 24:1304-1307
19. Krings M, Stone A, Schmitz R, Krainitzki H, Stoneking M, Pääbo S (1997) Neanderthal DNA sequences and the origin of modern humans. Cell 90:19-30
20. Lalueza-Fox C, Luna Calderón F, Calafell F, Morera B, Bertranpetit J (2001) mtDNA from extinct Tainos and the peopling of the Caribbean. Ann Hum Genet 65:137-151
21. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709-715
22. Loreille O, Orlando L, Patou-Mathis M, Philippe M, Taberlet P, Hänni C (2001) Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages. Curr Biol 11:200-203
23. Nielsen-Marsh C (2000) Patterns of diagenesis in bone. I. Effects of site environments. J Archeol Sci 27:1139-1150
24. Ovchinnikov I, Götherström A, Romanova G, Kharitonov V, Lidén K, Goodwin W (2000) Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404:490-493
25. Pääbo S (1989) Ancient DNA: Extraction, characterisation, molecular cloning and enzymatic amplification. Proc Natl Acad Sci USA 86:1939-1943
26. Pääbo S, Irwin D, Wilson A (1990) DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem 265:4718-4721
27. Pääbo S, Wilson AC (1991) Miocene DNA sequences - A dream come true? Curr Biol 1:45-46
28. Poinar H, Höss M, Bada J, Pääbo S (1996) Amino acid racemization and the preservation of ancient DNA. Science 272:864-866
29. Poinar HN, Kuch M, Sobolik KD, Barnes I, Stankiewicz AB, Kuder T, Spaulding WG, Bryant VM, Cooper A, Pääbo S (2001) A molecular analysis of dietary diversity for three archaic Native Americans. Proc Natl Acad Sci USA 98:4317-4322
30. Poinar H, Stankiewicz B (1999) Protein preservation and DNA retrieval from ancient tissues. Proc Natl Acad Sci USA 96:8426-8431
31. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with thermostable DNA polymerase. Science 239:487-491
32. Sanson GFO, Kawashita SY, Brunstein A, Briones MRS (2002) Experimental phylogeny of neutrally evolving DNA sequences generated by a bifurcate series of nested polymerase chain reactions. Mol Biol Evol 19:170-178
33. Smith CI, Chamberlain AT, Riley MS, Cooper A, Stringer CB, Collins MJ (2001) Neanderthal DNA: Not just old but old and cold? Nature 410:771-772
34. Tindall KR, Kunkel TA (1988) Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 27:6008-6013
35. Wallace DC, Lott MT, Brown MD, Huoponen K, Torroni A (1995) Report of the committee on human mitochondrial DNA. In: Cuticchia AJ (ed) Human Gene Mapping 1995: A Compendium. Johns Hopkins University Press, Baltimore, pp 910-954
36. Willerslev E, Hansen AJ, Christensen B, Steffensen JP, Arctander P (1999) Diversity of Holocene life forms in fossil glacier ice. Proc Natl Acad Sci USA 96:8017-8021
37. Yoshida M, Makino K, Morita H, Terato H, Ohyama Y, Ide H (1997) Substrate and mispairing properties of 5-formyl-2′-deoxyuridine 5′-triphosphate assessed by in vitro DNA polymerase reactions. Nucleic Acids Res 25:1570-1577
38. Zhang Q-M, Sugiyama H, Miyabe I, Matsuda S, Kino K, Saito I, Yonei S (1999) Replication in vitro and cleavage by restriction endonuclease of 5-formyluracil- and 5-hydroxymethyluracil-containing oligonucleotides. Int J Radiat Biol 75:59-65
39. Zhang Q-M, Sugiyama H, Miyabe I, Matsuda S, Saito I, Yonei S (1997) Replication of DNA templates containing 5-formyluracil, a major oxidative lesion of thymine in DNA. Nucleic Acids Res 25:3969-3973