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

Autor:	Seguin-Orlando A; Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark.; National High-throughput DNA Sequencing Centre, Øster Farimagsgade 2D, 1353K Copenhagen, Denmark., Gamba C; Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark., Sarkissian C; Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark., Ermini L; Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark., Louvel G; Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark., Boulygina E; National Research Centre Kurchatov Institute, 1, Akademika Kurchatova, Moscow, 123182, Russian Federation., Sokolov A; Centre Bioengineering, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/1, Moscow, 117312, Russian Federation., Nedoluzhko A; National Research Centre Kurchatov Institute, 1, Akademika Kurchatova, Moscow, 123182, Russian Federation., Lorenzen ED; Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark.; Department of Integrative Biology, University of California, Berkeley, CA 94720, USA., Lopez P; Department of Anthropology, Universidad de Chile, Ignacio Carrera Pinto 1045, Ñuñoa, Santiago, Chile., McDonald HG; Park Museum Management Program, National Park Service, 1201 Oakridge Drive, Suite 150, Fort Collins, Colorado 80525, USA., Scott E; San Bernardino County Museum, Division of Geological Sciences, 2024 Orange Tree Lane, Redlands, California 92374, USA., Tikhonov A; Zoological Institute of Russian Academy of Sciences, 199034 St. Petersburg, Russian Federation.; Institute of Applied Ecology of the North, North-Eastern Federal University, 677980 Yakutsk, Russian Federation., Stafford TW Jr; Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark., Alfarhan AH; Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia., Alquraishi SA; Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia., Al-Rasheid KAS; Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia., Shapiro B; Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Willerslev E; Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark., Prokhortchouk E; National Research Centre Kurchatov Institute, 1, Akademika Kurchatova, Moscow, 123182, Russian Federation., Orlando L; Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark.; Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 allées Jules Guesde, 31000 Toulouse, France.
Jazyk:	angličtina
Zdroj:	Scientific reports [Sci Rep] 2015 Jul 02; Vol. 5, pp. 11826. Date of Electronic Publication: 2015 Jul 02.
DOI:	10.1038/srep11826
Abstrakt:	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.
Databáze:	MEDLINE
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