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  • Pros and cons of methylation-based enrichment methods for ancient DNA

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    Author(s)
    Seguin-Orlando, Andaine
    Gamba, Cristina
    Der Sarkissian, Clio
    Ermini, Luca
    Louvel, Guillaume
    Boulygina, Eugenia
    Sokolov, Alexey
    Nedoluzhko, Artem
    Lorenzen, Eline D.
    Lopez, Patricio
    McDonald, H. Gregory
    Scott, Eric
    Tikhonov, Alexei
    Stafford Jr, Thomas W.
    Alfarhan, Ahmed H.
    Alquraishi, Saleh A.
    Al-Rasheid, Khaled A. S.
    Shapiro, Beth
    Willerslev, Eske
    Prokhortchouk, Egor
    Orlando, Ludovic
    Griffith University Author(s)
    Willerslev, Eske
    Year published
    2015
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    Abstract
    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally ...
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    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.
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    Journal Title
    Scientific Reports
    Volume
    5
    DOI
    https://doi.org/10.1038/srep11826
    Copyright Statement
    © The Author(s) 2015. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
    Subject
    Biochemistry and Cell Biology not elsewhere classified
    Publication URI
    http://hdl.handle.net/10072/172168
    Collection
    • Journal articles

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