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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-12

AUTHORS

Andaine Seguin-Orlando, Cristina Gamba, Clio Der Sarkissian, Luca Ermini, Guillaume Louvel, Eugenia Boulygina, Alexey Sokolov, Artem Nedoluzhko, Eline D Lorenzen, Patricio Lopez, H Gregory McDonald, Eric Scott, Alexei Tikhonov, Thomas W Stafford, Ahmed H Alfarhan, Saleh A Alquraishi, Khaled A S Al-Rasheid, Beth Shapiro, Eske Willerslev, Egor Prokhortchouk, Ludovic Orlando

ABSTRACT

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. More... »

PAGES

11826

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/srep11826

DOI

http://dx.doi.org/10.1038/srep11826

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1046888835

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/26134828


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448 https://www.grid.ac/institutes/grid.443909.3 schema:alternateName University of Chile
449 schema:name Department of Anthropology, Universidad de Chile, Ignacio Carrera Pinto 1045, Ñuñoa, Santiago, Chile.
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451 https://www.grid.ac/institutes/grid.454846.f schema:alternateName National Park Service
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455 schema:name Centre Bioengineering, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/1, Moscow, 117312, Russian Federation.
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458 schema:name 1] Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark [2] National High-throughput DNA Sequencing Centre, Øster Farimagsgade 2D, 1353K Copenhagen, Denmark.
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461 https://www.grid.ac/institutes/grid.56302.32 schema:alternateName King Saud University
462 schema:name Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
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