Improved detection of methylation in ancient DNA.

Ancient DNA Bisulfite treatment Enzymatic methylation treatment Methylation Paleogenomics

Journal

Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660

Informations de publication

Date de publication:
10 Oct 2024
Historique:
received: 20 12 2023
accepted: 26 09 2024
medline: 11 10 2024
pubmed: 11 10 2024
entrez: 10 10 2024
Statut: epublish

Résumé

Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.

Identifiants

pubmed: 39390557
doi: 10.1186/s13059-024-03405-5
pii: 10.1186/s13059-024-03405-5
doi:

Substances chimiques

DNA, Ancient 0
Sulfites 0
hydrogen sulfite OJ9787WBLU

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

261

Informations de copyright

© 2024. The Author(s).

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Auteurs

Susanna Sawyer (S)

Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. susanna.sawyer@univie.ac.at.
Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. susanna.sawyer@univie.ac.at.

Pere Gelabert (P)

Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.

Benjamin Yakir (B)

Department of Statistics, The Faculty of Social Science, The Hebrew University Mount Scopus, Jerusalem, Israel.

Alejandro Llanos-Lizcano (A)

Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
Facultad de Química y Farmacia, Universidad del Atlántico, Barranquilla, Colombia.

Alessandra Sperduti (A)

Museo Delle Civiltà, Servizio Di Bioarcheologia, Rome, Italy.
Dipartimento di Asia, Africa e Mediterraneo, Università degli Studi di Napoli "L'Orientale", Naples, Italy.

Luca Bondioli (L)

Università Di Padova, Dipartimento Dei Beni Culturali, Padua, Italy.

Olivia Cheronet (O)

Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.

Christine Neugebauer-Maresch (C)

Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria.
Institute of Prehistory and Early History, University of Vienna, Vienna, Austria.

Maria Teschler-Nicola (M)

Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
Department of Anthropology, Natural History Museum Vienna, Vienna, Austria.

Mario Novak (M)

Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia.
Department of Archaeology and Heritage, Faculty of Humanities, University of Primorska, Koper, Slovenia.

Ildikó Pap (I)

Department of Biological Anthropology, Institute of Biology, University of Szeged, Szeged, Hungary.
Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary.
Department of Biological Anthropology, Eötvös Loránd University, Budapest, Hungary.

Ildikó Szikossy (I)

, Budapest, Hungary.

Tamás Hajdu (T)

Department of Biological Anthropology, Eötvös Loránd University, Budapest, Hungary.

Vyacheslav Moiseyev (V)

Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), RAS, Saint Petersburg, Russia.

Andrey Gromov (A)

Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), RAS, Saint Petersburg, Russia.

Gunita Zariņa (G)

Institute of Latvian History, University of Latvia, Riga, Latvia.

Eran Meshorer (E)

The Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel.
Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.

Liran Carmel (L)

Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.

Ron Pinhasi (R)

Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. ron.pinhasi@univie.ac.at.
Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. ron.pinhasi@univie.ac.at.

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