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dc.contributor.authorPedersen, Jakob Skou
dc.contributor.authorValen, Eivind
dc.contributor.authorVelazquez, Amhed M. V.
dc.contributor.authorParker, Brian J.
dc.contributor.authorRasmussen, Morten
dc.contributor.authorLindgreen, Stinus
dc.contributor.authorLilje, Berit
dc.contributor.authorTobin, Desmond J.
dc.contributor.authorKelly, Theresa K.
dc.contributor.authorVang, Soren
dc.contributor.authorAndersson, Robin
dc.contributor.authorJones, Peter A.
dc.contributor.authorHoover, Cindi A.
dc.contributor.authorTikhonov, Alexei
dc.contributor.authorProkhortchouk, Egor
dc.contributor.authorRubin, Edward M.
dc.contributor.authorSandelin, Albin
dc.contributor.authorGilbert, M. Thomas P.
dc.contributor.authorKrogh, Anders
dc.contributor.authorWillerslev, Eske
dc.contributor.authorOrlando, Ludovic
dc.date.accessioned2017-12-04T06:20:39Z
dc.date.available2017-12-04T06:20:39Z
dc.date.issued2014
dc.identifier.issn1088-9051
dc.identifier.doi10.1101/gr.163592.113
dc.identifier.urihttp://hdl.handle.net/10072/172207
dc.description.abstractEpigenetic 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.
dc.description.peerreviewedYes
dc.languageEnglish
dc.language.isoeng
dc.publisherCold Spring Harbor Laboratory Press
dc.relation.ispartofpagefrom454
dc.relation.ispartofpageto466
dc.relation.ispartofissue3
dc.relation.ispartofjournalGenome Research
dc.relation.ispartofvolume24
dc.subject.fieldofresearchGenetics not elsewhere classified
dc.subject.fieldofresearchBiological Sciences
dc.subject.fieldofresearchMedical and Health Sciences
dc.subject.fieldofresearchcode060499
dc.subject.fieldofresearchcode06
dc.subject.fieldofresearchcode11
dc.titleGenome-wide nucleosome map and cytosine methylation levels of an ancient human genome
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
dcterms.licensehttp://creativecommons.org/licenses/by-nc/3.0/
dc.description.versionVersion of Record (VoR)
gro.rights.copyright© The Author(s) 2014. This is an Open Access article distributed under the terms of the Creative Commons CC-BY-NC License (Attribution-NonCommercial 3.0 Unported License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
gro.hasfulltextFull Text
gro.griffith.authorWillerslev, Eske


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