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    Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    Access Status
    Open access via publisher
    Authors
    Pedersen, J.
    Valen, E.
    Velazquez, A.
    Parker, B.
    Rasmussen, M.
    Lindgreen, S.
    Lilje, B.
    Tobin, D.
    Kelly, T.
    Vang, S.
    Andersson, R.
    Jones, P.
    Hoover, C.
    Tikhonov, A.
    Prokhortchouk, E.
    Rubin, E.
    Sandelin, A.
    Gilbert, Thomas
    Krogh, A.
    Willerslev, E.
    Orlando, L.
    Date
    2014
    Type
    Journal Article
    
    Metadata
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    Citation
    Pedersen, J. and Valen, E. and Velazquez, A. and Parker, B. and Rasmussen, M. and Lindgreen, S. and Lilje, B. et al. 2014. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Research. 24: pp. 454-466.
    Source Title
    Genome Research
    DOI
    10.1101/gr.163592.113
    ISSN
    1088-9051
    URI
    http://hdl.handle.net/20.500.11937/48012
    Collection
    • Curtin Research Publications
    Abstract

    Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next generation sequence reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a four thousand year old Palaeo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues. Using ancient methylation information we estimated the age at death of the Saqqaq individual and illustrate how epigenetic information can be used to infer ancient gene expression. Similar epigenetic signatures were found in other fossil material, such as 110-130 kyr-old bones, supporting the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time as well as providing an original window into modern epigenomics.

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