Neandertal Methyl Track Settings
Neandertal Reconstructed DNA Methylation Map   (All Neandertal Assembly and Analysis tracks)

Display mode:      Duplicate track
View table schema
Data last updated at UCSC: 2014-08-28


This track shows the reconstructed DNA methylation map of the Neandertal genome, derived from bone tissues.

Display conventions and configuration

Green to red scaling is used as a rough indicator of methylation. Values range from 0% (green, unmethylated) to 100% (red, methylated). Data are displayed for CpG positions across the genome.


Gokhman et al. reconstructed the DNA methylation maps of two archaic humans, the Neandertal and the Denisovan, based on the natural deamination of cytosines in ancient DNA. With time, cytosines (C's) in post-mortem DNA lose their amine group (deamination). However, deamination of methylated vs. unmethylated C's results in different products - Methylated C's are deaminated with time to T's, whereas unmethylated C's are deaminated to U's. The U's are later removed during ancient DNA library preparation and as a result, a distinct pattern is observed: methylated regions in the genome display high C-->T conversion rate, whereas unmethylated regions display a low C-->T conversion rate. These patterns were used to reconstruct the full DNA methylation maps of the archaic humans.


This track was produced at UCSC using data generated by Gokhman et al., 2014.


Gokhman D, Lavi E, Prüfer K, Fraga MF, Riancho JA, Kelso J, Pääbo S, Meshorer E, Carmel L. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science. 2014 May 2;344(6183):523-7. PMID: 24786081