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

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 dat...

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Bibliographic Details
Published in:Genome Research
Main 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.
Format: Article in Journal/Newspaper
Language:unknown
Published: Cold Spring Harbor Laboratory Press 2014
Subjects:
Cytosine methylation
Nucleosome map
Ancient DNA
Epigenomics
eskimo*
Saqqaq
Saqqaq culture
Online Access:https://hdl.handle.net/20.500.11937/48012
https://doi.org/10.1101/gr.163592.113
Description
Summary: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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