Pros and cons of methylation-based enrichment methods for ancient DNA

• Published in: Scientific Reports
• Main Authors: Seguin Orlando, Andaine, Gamba, Cristina, Sarkissian, Clio Der, Ermini, Luca, Louvel, Guillaume, Boulygina, Eugenia, Sokolov, Alexey, Nedoluzhko, Artem, Lorenzen, Eline D., López, Patricio, McDonald, H. Gregory, Scott, Eric, Tikhonov, Alexei, Stafford, Thomas W., Alfarhan, Ahmed H., Alquraishi, Saleh A., Al-Rasheid, Khaled A. S., Shapiro, Beth, Willerslev, Eske, Prokhortchouk, Egor, Orlando, Ludovic
• Format: Article in Journal/Newspaper
• Language: English
• Published: Nature Publishing 2015
• Subjects: Complete mitochondrial genome; Sequencing libraries; CPG islands; Horse; Capture; Reveal; Polar; Amplification; Evolutionary; Neanderthal; Isi; eskimo*; Saqqaq
• Online Access: https://doi.org/10.1038/srep11826; https://repositorio.uchile.cl/handle/2250/133888

Artículo de publicación ISI The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions. Marie-Curie Career Integration grant FP7 CIG-293845 International Research Group Program, Deanship of Scientific Research (King Saud University, Saudi Arabia) IRG14-08 Marie-Curie Intra-European Fellowships FP7-IEF-328024 FP7 IEF-302617 Danish National Research Foundation DNRF94