Inferring DNA methylation in non-skeletal tissues of ancient specimens

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• dc.contributor.author Mathov, Yoav
• dc.contributor.author Nissim Rafinia, Malka
• dc.contributor.author Leibson, Chen
• dc.contributor.author Galun, Nir
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-
• dc.contributor.author Kandel, Arye
• dc.contributor.author Liebergal, Meir
• dc.contributor.author Meshorer, Eran
• dc.contributor.author Carmel, Liran
• dc.date.accessioned 2025-01-15T07:36:19Z
• dc.date.available 2025-01-15T07:36:19Z
• dc.date.issued 2024
• dc.description Data de publicació eelctrònica: 20-11-2024
• dc.description.abstract Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes.
• dc.description.sponsorship This publication was made possible through the support of a grant from the John Templeton Foundation (grant ID 61739 to L.C. and E.M.). The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. This study was also funded by the Israel Science Foundation (grant no. 2436/22 to L.C.) and by the Ministry of Innovation, Science & Technology (grant no. grant 1001584586 to L.C. and E.M.). T.M.-B. is supported by funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864203), PID2021-126004NB-100 (MICIIN/FEDER, UE), ‘Unidad de Excelencia María de Maeztu’, funded by the AEI (CEX2018-000792-M), NIH 1R01HG010898-01A1 and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2021 SGR 00177). L.C. is the Snyder Granadar chair in Genetics. E.M. is the Arthur Gutterman Family Chair for Stem Cell Research. We wish to thank Avigal Be’er for the design of Fig. 1.
• dc.format.mimetype application/pdf
• dc.identifier.citation Mathov Y, Nissim-Rafinia M, Leibson C, Galun N, Marques-Bonet T, Kandel A, et al. Inferring DNA methylation in non-skeletal tissues of ancient specimens. Nat Ecol Evol. 2024 Nov 20. DOI: 10.1038/s41559-024-02571-w
• dc.identifier.doi http://dx.doi.org/10.1038/s41559-024-02571-w
• dc.identifier.issn 2397-334X
• dc.identifier.uri http://hdl.handle.net/10230/69133
• dc.language.iso eng
• dc.publisher Nature Research
• dc.relation.ispartof Nat Ecol Evol. 2024 Nov 20
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2021-126004NB-100
• dc.rights © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/
• dc.subject.keyword Epigenetics
• dc.subject.keyword Epigenomics
• dc.subject.keyword Evolutionary genetics
• dc.title Inferring DNA methylation in non-skeletal tissues of ancient specimens
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion