Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.
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2014Author
Pedersen, J.S.Valen, E.
Velazquez, A.M.V.
Parker, B.J.
Lindgreen, S.
Lilje, B.
Tobin, Desmond J.
Kelly, T.K.
Vang, S.
Andersson, R.
Jones, P.A.
Hoover, C.A.
Prokhortchouk, E.
Rubin, E.M.
Sandelin, A.
Gilbert, M.T.P.
Krogh, A.
Willerslev, E.
Keyword
Epigenetic informationGenome-wide survey
Nucleosome map
Cytosine methylation levels
Ancient human genome
Rights
2014 Pedersen et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.Peer-Reviewed
YesOpen Access status
openAccess
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Show full item recordAbstract
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 4000-yr-old Paleo- 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 110,000- to 130,000-yr-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.Version
Published versionCitation
Pedersen, J. S., Valen, E., Velazquez, A.M., Parker, B.J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D.J., Kelly, T.K., Vang, S., Andersson, R., Jones, P.A., Hoover, C.A., Tikhonov, A., Prokhortchouk, E., Rubin, E.M., Sandelin, A., Gilbert, M.T., Krogh, A., Willerslev, E. and Orlando, L. (2014) Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Research, 24 (3): 454-66.Link to Version of Record
https://doi.org/10.1101/gr.163592.113Type
Articleae974a485f413a2113503eed53cd6c53
https://doi.org/10.1101/gr.163592.113