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

ABSTRACT: 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 ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-ch

SUBMITTER: Hanghoj K 

PROVIDER: S-EPMC5100044 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature