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Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage

hal.structure.identifierCentre d'anthropologie et de génomique de Toulouse [CAGT]
hal.structure.identifierCentre National de Ressources Génomiques Végétales [CNRGV]
dc.contributor.authorWAGNER, Stefanie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierCentre d'anthropologie et de génomique de Toulouse [CAGT]
hal.structure.identifierIT University of Copenhagen [ITU]
dc.contributor.authorORLANDO, Ludovic
dc.date.issued2020-01-31
dc.identifier.issn2296-701X
dc.description.abstractEnThe ultra-short DNA molecules still preserved in archeological remains can provide invaluable genetic information about past individuals, species, and communities within the half to 1-million-year time range. The sequence data are, however, generally affected by post-mortem DNA damage and include specific patterns of nucleotide mis-incorporations, which can help data authentication. Recent work in ancient mammals has shown that such patterns can also help assess past levels of DNA methylation in CpG contexts. Despite pioneering work in barley and sorghum, ancient epigenetic marks have received limited attention in plants and it remains unknown whether ancient epigenetic signatures can be retrieved in any of the three main sequence contexts (CG, CHG, and CHH). To address this question, we extended a statistical methylation score originally proposed to trace cytosine methylation in mammal sequence data to accommodate the three methylation contexts common in plants. We applied this score to a range of tissues (wood, cobs, and grains) and species (oak, maize, and barley), spanning both desiccated and waterlogged archeological samples. Ancient sequence data obtained for USER-treated DNA extracts yielded methylation scores on par with DNA methylation levels of modern organellar and nuclear genomes. At the quantitative level, scores were (1) positively correlated to post-mortem cytosine deamination, and (2) replicated relative contributions of CG, CHG, and CHH contexts to DNA methylation assessed by bisulfite DNA sequencing of modern plant tissues. This demonstrates that genuine DNA methylation signatures can be characterized in ancient plant remains, which opens new avenues for investigating the plant evolutionary response to farming, pollution, epidemics, and changing environmental conditions.
dc.description.sponsorshipImpacts évolutif et fonctionnel de variations épigénétiques chez des arbres forestiers. - ANR-17-CE32-0009
dc.language.isoen
dc.publisherFrontiers Media
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enancient DNA
dc.subject.enDNA methylation
dc.subject.engenomics
dc.subject.enpost-mortem DNA damage
dc.subject.enoakmaize
dc.subject.enbarley
dc.title.enUncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage
dc.typeArticle de revue
dc.identifier.doi10.3389/fevo.2020.00011
dc.subject.halSciences de l'environnement
bordeaux.journalFrontiers in Ecology and Evolution
bordeaux.page11
bordeaux.volume8
bordeaux.peerReviewedoui
hal.identifierhal-04781081
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-04781081v1
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