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Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

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Briggs, Adrian W., Stenzel, Udo, Meyer, Matthias, Krause, Johannes, Kircher, Martin, Pääbo, Svante·2010·Nucleic Acids Research
DOI 10.1093/nar/gkp1163PMC PMC2847228
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Abstract

DNA sequences determined from ancient organisms have high error rates, primarily due to uracil bases created by cytosine deamination. We use synthetic oligonucleotides, as well as DNA extracted from mammoth and Neandertal remains, to show that treatment with uracil-DNA-glycosylase and endonuclease VIII removes uracil residues from ancient DNA and repairs most of the resulting abasic sites, leaving undamaged parts of the DNA fragments intact. Neandertal DNA sequences determined with this protocol have greatly increased accuracy. In addition, our results demonstrate that Neandertal DNA retains in vivo patterns of CpG methylation, potentially allowing future studies of gene inactivation and imprinting in ancient organisms.

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  • The UDG treatment strategy is inefficient at removing terminal uracils, allowing the mismatch rate to the human genome at the terminal nucleotide to be used for authentication.

    “The UDG treatment strategy is (by-design) inefficient at removing terminal uracils, allowing the mismatch rate to the human genome at the terminal nucleotide to be used for authentication38.”

    From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [38]

    The Results (Repair of Neandertal DNA) say UDG/endoVIII treatment drastically reduced end-of-fragment C/G→T/A mismatches, with removal almost complete in mtDNA. The Results (Neandertal CpG methylation) attribute most remaining terminal C→T mismatches in nuclear DNA to CpG sites, not to deliberately inefficient removal of terminal uracils. The paper does not describe preserving terminal mismatches for authentication. (LLM, conf=0.87)

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  • All the libraries analyzed had rates of C-to-T substitution in the final nucleotide of at least 3%, consistent with genuine ancient DNA.

    “We quantified the rate of C-to-T substitution in the final nucleotide of the sequences analyzed, relative to the human reference genome sequence, and found that all the libraries analyzed had rates of at least 3%38, consistent with genuine ancient DNA.”

    From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [38]

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Authors
Briggs, A. W., Stenzel, U., Meyer, M., Krause, J., Kircher, M., & Pääbo, S.
Affiliations
Max Planck Society (DE)
Corresponding author
Briggs, Adrian W.
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2009-12-22
Volume
38
Issue
6
Pages
e87-e87
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkp1163
PMC
PMC2847228
OpenAlex
W1993435119
Cited by
491
References
1
Citations by year
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FWCI
9.75
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
  • Max Planck Institute for Plasma Physics (submittedVersion)
  • Max Planck Digital Library (submittedVersion, other-oa)
  • MPG.PuRe (Max Planck Society) (submittedVersion, cc-by-nc)
Funders
Hrvatska Akademija znanosti i umjetnosti
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
ancient DNA, cytosine deamination, uracil-DNA glycosylase, endonuclease VIII, CpG methylation, gene inactivation, genomic imprinting
MeSH terms
Animals, Cytosine, Deamination, DNA Repair, Humans, Oligonucleotides, Hominidae, Sequence Analysis, DNA, CpG Islands, DNA Methylation, Deoxyribonuclease (Pyrimidine Dimer), Uracil-DNA Glycosidase, Mammoths

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