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

@article{Pedersen2014GenomewideNM,
  title={Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.},
  author={Jakob Skou Pedersen and Eivind Valen and Amhed Missael Vargas Velazquez and Brian J. Parker and Morten Rasmussen and Stinus Lindgreen and Berit Lilje and Desmond J. Tobin and Theresa K. Kelly and S{\o}ren Vang and Robin Andersson and Peter A. Jones and Cindi A. Hoover and Alexei N. Tikhonov and Egor Prokhortchouk and Edward M. Rubin and Albin Sandelin and M. Thomas P. Gilbert and Anders Krogh and Eske Willerslev and Ludovic Orlando},
  journal={Genome research},
  year={2014},
  volume={24 3},
  pages={
          454-66
        }
}
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… 

Figures from this paper

Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan

Insight is provided into the epigenetic landscape of the authors' closest evolutionary relatives and a window is opened to explore the epigenomes of extinct species by harnessing the natural degradation processes of methylated and unmethylated cytosines.

Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage

It is demonstrated that genuine DNA methylation signatures can be characterized in ancient plant remains, which opens new avenues for investigating the plant evolutionary response to farming, pollution, epidemics, and changing environmental conditions.

Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX

The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which

DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage

DamMet is presented, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data that builds on a novel statistical model of post-mortem DNA damage for dinucleotides, accounting for sequencing errors, genotypes, and differential post- autopsy cytosine deamination rates at both methylated and unmethylated sites.

Assessing DNA Sequence Alignment Methods for Characterizing Ancient Genomes and Methylomes

A read alignment strategy making use of the Bowtie2 aligner that substantially reduce computational times but shows increased sensitivity relative to previous recommendations based on the BWA aligner is identified, which significantly improves the genome coverage especially when DNA templates are shorter than 90 bp, as is typically the case for ancient DNA.

Epigenetics of Ancient DNA

Improvement of methodological approaches to genome-wide analysis has opened up new possibilities in the search for the epigenetic mechanisms involved in the regulation of gene expression, and it is demonstrated that it is possible to determine the transcriptional activity of genes in ancient DNA samples by combining information on DNA methylation and the DNAaseI hypersensitive sequences located at the transcription start sites of genes.

Epigenetics and evolution.

This article revisits historical as well as recent studies that indicate significant impacts of epigenetic processes on evolution and main focus is DNA methylation, which is a prevalent chemical modification of genomic DNA.

Impact of DNA methylation on 3D genome structure

Results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal.

Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns

Abstract Recent developments in high-throughput sequencing (HTS) technologies have enabled the reconstruction of complete genome sequence and nucleosome and methylation maps from ancient individuals.

DNA methylation profiling in mummified human remains from the eighteenth-century

This study determined if EPIC Illumina BeadChip technology is applicable for specimens from mummies of the eighteenth century CE and provided proof of principle that Illumina beadChips are applicable for DNAm profiling in ancient samples.
...

References

SHOWING 1-10 OF 91 REFERENCES

High-Resolution Analysis of Cytosine Methylation in Ancient DNA

The ability to resolve cytosine methylation in ancient DNA provides a powerful means to study the role of epigenetics in evolution, and establishes the biochemical stability of methylated cytosines over extensive time frames.

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Low-throughput reduced representation bisulphite sequencing is established as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.

NOMe-seq gives the first genome-wide DNA methylation and nucleosome positioning correlation at the single molecule, and thus, single cell level, that can be used to monitor disease progression and response to therapy.

Developmental programming of CpG island methylation profiles in the human genome

It is shown that unmethylated regions (UMRs) seem to be formed during early embryogenesis, not as a result of CpG-ness, but rather through the recognition of specific sequence motifs closely associated with transcription start sites.

Finding the fifth base: genome-wide sequencing of cytosine methylation.

Advanced "next-generation" DNA sequencing technologies are now enabling the global mapping of this epigenetic modification at single-base resolution, providing new insights into the regulation and dynamics of DNA methylation in genomes.

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing

Dense methylation surrounding the transcription start site (TSS) is uncoupled from methylation within more downstream regions suggesting that there are at least two classes of intragenic methylation, and direct evidence that DNA methylation is interpreted dissimilarly in different regions of the gene body is provided.

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

An array of well-positioned nucleosomes flanking sites occupied by the insulator binding protein CTCF across the human genome is discovered, suggesting that binding of CTCf provides an anchor point for positioning nucleosome, and chromatin remodeling is an important component of C TCF function.

Controls of Nucleosome Positioning in the Human Genome

A large fraction of nucleosomes are consistently positioned—in some regions because they adopt favored sequence positions, and in other regions becausethey are forced into specific arrangements by chromatin remodeling or DNA binding proteins.

Dynamic changes in the human methylome during differentiation.

A whole-genome comparative view of DNA methylation using bisulfite sequencing of three cultured cell types representing progressive stages of differentiation highlights the value of high-resolution methylation maps, in conjunction with other systems-level analyses, for investigation of previously undetectable developmental regulatory mechanisms.
...