TY - JOUR
T1 - Pros and cons of methylation-based enrichment methods for ancient DNA
AU - Seguin-Orlando, Andaine
AU - Gamba, Cristina
AU - Der Sarkissian, Clio
AU - Ermini, Luca
AU - Louvel, Guillaume
AU - Boulygina, Eugenia
AU - Sokolov, Alexey
AU - Nedoluzhko, Artem
AU - Lorenzen, Eline
AU - Lopez, Patricio
AU - McDonald, H. Gregory
AU - Scott, Eric
AU - Tikhonov, Alexei
AU - Stafford jr., Thomas
AU - Alfarhan, Ahmed H.
AU - Alquraishi, Saleh A.
AU - Al-Rasheid, Khaled A. S.
AU - Shapiro, Beth
AU - Willerslev, Eske
AU - Prokhortchouk, Egor
AU - Orlando, Ludovic Antoine Alexandre
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
U2 - 10.1038/srep11826
DO - 10.1038/srep11826
M3 - Journal article
C2 - 26134828
AN - SCOPUS:84934783998
VL - 5
JO - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
M1 - 11826
ER -