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Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.
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.
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.
Publication Date
2014
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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/.
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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 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.
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Citation
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.
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