ArticleGenome research2014
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
67 citing papers in PubMed, 1 synthesis or guideline pooled it, 184 citations in OpenAlex.
- A Beginner's Guide for Using Bone in Marine Mammal Research.Integrative and comparative biology · 2026Guideline
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- Naturally-occurring DNA fragment termini correlate with methylation at CpG sites in hair and blood plasma cell-free DNA.BMC genomics · 2026Article
- Rootless hair as a reliable source of forensic genetic information.Genome biology · 2026Article
- The rise of historical epigenomics and temporal analysis of gene regulation.Genome biology · 2025Review
- RoAM: computational reconstruction of ancient methylomes and identification of differentially methylated regions.Genome biology · 2025Article
- Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies.Molecular ecology resources · 2025Review
- Inferring DNA methylation in non-skeletal tissues of ancient specimens.Nature ecology & evolution · 2025Article
- Allele-specific DNA demethylation editing leads to stable upregulation of allele-specific gene expression.iScience · 2024Article
- Century-old chromatin architecture revealed in formalin-fixed vertebrates.Nature communications · 2024Article
- Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.Cell · 2024Article
- Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise.Evolutionary applications · 2024Article
- Unravelling reference bias in ancient DNA datasets.Bioinformatics (Oxford, England) · 2024Article
- Human brains preserve in diverse environments for at least 12 000 years.Proceedings. Biological sciences · 2024Article
- Reconstructing DNA methylation maps of ancient populations.Nucleic acids research · 2024Article
- Article
- Development of super-specific epigenome editing by targeted allele-specific DNA methylation.Epigenetics & chromatin · 2023Article
- Deep-time paleogenomics and the limits of DNA survival.Science (New York, N.Y.) · 2023Review
- DNA methylation-based profiling of horse archaeological remains for age-at-death and castration.iScience · 2023Article
- CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.PLoS computational biology · 2022Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors at 6 institutions in 5 countries.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.