Pedersen, Jakob Skou3; Valen, Eivind8; Velazquez, Amhed Missael Vargas4; Parker, Brian John9; Rasmussen, Morten10; Lindgreen, Stinus11; Lilje, Berit8; Tobin, Desmond J.4; Kelly, Theresa K.4; Vang, Søren3; Andersson, Robin8; Jones, Peter A.4; Hoover, Cindi A.4; Tikhonov, Alexei4; Prokhortchouk, Egor4; Rubin, Edward M.4; Sandelin, Albin Gustav8; Gilbert, M. Thomas P.12; Krogh, Anders8; Willerslev, Eske12; Orlando, Ludovic Antoine Alexandre12
1 Computational and RNA Biology, Department of Biology, Faculty of Science, Københavns Universitet2 Natural History Museum of Denmark, Natural History Museum of Denmark, Faculty of Science, Københavns Universitet3 Aarhus Universitet4 unknown5 Department of Mathematical Sciences, Faculty of Science, Københavns Universitet6 Natural History Museum of Denmark, Faculty of Science, Københavns Universitet7 Department of Biology, Faculty of Science, Københavns Universitet8 Computational and RNA Biology, Department of Biology, Faculty of Science, Københavns Universitet9 Department of Mathematical Sciences, Faculty of Science, Københavns Universitet10 Natural History Museum of Denmark, Faculty of Science, Københavns Universitet11 Department of Biology, Faculty of Science, Københavns Universitet12 Natural History Museum of Denmark, Natural History Museum of Denmark, Faculty of Science, Københavns Universitet
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.
Genome Research, 2014, Vol 24, Issue 3, p. 454-466