Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan

@article{Gokhman2014ReconstructingTD,
  title={Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan},
  author={David Gokhman and Eitan Lavi and Kay Pr{\"u}fer and Mario Fern{\'a}ndez Fraga and Jos{\'e} A. Riancho and Janet Kelso and Svante P{\"a}{\"a}bo and Eran Meshorer and Liran Carmel},
  journal={Science},
  year={2014},
  volume={344},
  pages={523 - 527}
}
Methylating the Family Tree DNA sequences show a high level of similarities between humans and ancient hominids but the degree to which there are differences between methylated regions in their genomes that may explain phenotypic differences is unclear. Gokhman et al. (p. 523, published online 17 April) demonstrate that naturally degraded methylated cytosines in ancient DNA are converted to thymines and can be used to reconstruct ancient methylomes. The results suggest differences in… 
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References

SHOWING 1-10 OF 47 REFERENCES
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.
TLDR
It is shown that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains, laying 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.
Dynamics of DNA Methylation in Recent Human and Great Ape Evolution
TLDR
It is concluded that epigenetic alterations are an important force during primate evolution and have been under-explored in evolutionary comparative genomics.
A High-Coverage Genome Sequence from an Archaic Denisovan Individual
TLDR
The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size, and illuminates the relationships between humans and archaics, including Neandertals, and establishes a catalog of genetic changes within the human lineage.
Understanding the recent evolution of the human genome: insights from human–chimpanzee genome comparisons
TLDR
Recent progress in comparing the human and chimpanzee genomes is reviewed and how the differences detected have improved the understanding of the evolution of the human genome is discussed.
Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
TLDR
The results demonstrate that Neandertal DNA retains in vivo patterns of CpG methylation, potentially allowing future studies of gene inactivation and imprinting in ancient organisms.
DNA methylation: roles in mammalian development
TLDR
Key concepts in the function of DNA methylation in mammals are discussed, stemming from more than two decades of research, including many recent studies that have elucidated when and whereDNA methylation has a regulatory role in the genome.
Functions of DNA methylation: islands, start sites, gene bodies and beyond
TLDR
Improved genome-scale mapping of methylation allows us to evaluate DNA methylation in different genomic contexts: transcriptional start sites with or without CpG islands, in gene bodies, at regulatory elements and at repeat sequences.
The complete genome sequence of a Neandertal from the Altai Mountains
TLDR
It is shown that interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene and a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans is established.
Integrative Analysis Reveals Relationships of Genetic and Epigenetic Alterations in Osteosarcoma
TLDR
Integrative analysis of genome-wide genetic and epigenetic alterations identified dependencies and relationships between DNA copy number, DNA methylation and mRNA expression in osteosarcomas, contributing to better understanding of osteosARcoma biology.
Association of H19 promoter methylation with the expression of H19 and IGF-II genes in adrenocortical tumors.
TLDR
The results suggest that altered DNA methylation of the H19 promoter is involved in the abnormal expression of both H19 and IGF-II genes in human adrenocortical carcinomas.
...
...