Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
MetadataShow full item record
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 four thousand year old Palaeo-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 110-130 kyr-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.
Showing items related by title, author, creator and subject.
Nustad, H.; Almeida, M.; Canty, A.; Leblanc, M.; Page, C.; Melton, Phillip (2018)© 2018 The Author(s). Background: Longitudinal data and repeated measurements in epigenome-wide association studies (EWAS) provide a rich resource for understanding epigenetics. We summarize 7 analytical approaches to the ...
Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemiaRani, L.; Mathur, N.; Gupta, Ritu; Gogia, A.; Kaur, G.; Dhanjal, J.; Sundar, D.; Kumar, L.; Sharma, A. (2017)Â© 2017, The Author(s). Background: In chronic lymphocytic leukemia (CLL), epigenomic and genomic studies have expanded the existing knowledge about the disease biology and led to the identification of potential biomarkers ...
Zhang, Y.; Florath, Ines; Saum, K.; Brenner, H. (2016)BACKGROUND: Epigenome-wide profiling of DNA methylation pattern with respect to tobacco smoking has given rise to a new measure of smoking exposure. We investigated the relationships of methylation markers with both ...