Pedersen, Jakob Skou16; Valen, Eivind2; Velazquez, Amhed M Vargas3; Parker, Brian John4; Rasmussen, Morten3; Lindgreen, Stinus5; Lilje, Berit2; Tobin, Desmond J6; Kelly, Theresa K7; Vang, Søren16; Andersson, Robin2; Jones, Peter A8; Hoover, Cindi A9; Tikhonov, Alexei10; Prokhortchouk, Egor11; Rubin, Edward M12; Sandelin, Albin Gustav2; Gilbert, M Thomas P13; Krogh, Anders14; Willerslev, Eske15; Orlando, Ludovic Antoine Alexandre15
1 Department of Clinical Medicine - Molekylær Medicinsk afdeling (MOMA), Department of Clinical Medicine, Health, Aarhus University2 Bioinformatics3 Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.4 Institut for Matematiske Fag5 Biologisk Institut6 Centre for Skin Sciences, School of Life Sciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, United Kingdom7 Department of Urology, Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-9181, USA8 Department of Urology, Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-9181, USA9 DOE Joint Genome Institute, Walnut Creek, California 94598, USA10 Zoological Institute of Russian Academy of Sciences, 199034 St. Petersburg, Russian Federation11 Center “Bioengineering” of the Russian Academy of Sciences, 117312 Moscow, Russian Federation12 DOE Joint Genome Institute, Walnut Creek, California 94598, USA13 Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark14 The Bioinformatics Centre, Department of Biology and the Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen N, Denmark15 Statens Naturhistoriske Museum16 Department of Clinical Medicine - Molekylær Medicinsk afdeling (MOMA), Department of Clinical Medicine, Health, Aarhus University
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