Pros and cons of methylation-based enrichment methods for ancient DNA.
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 containin...
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ftcdlib:oai:escholarship.org:ark:/13030/qt0d70r11c 2023-05-15T16:07:20+02:00 Pros and cons of methylation-based enrichment methods for ancient DNA. Seguin-Orlando, Andaine Gamba, Cristina Sarkissian, Clio Der Ermini, Luca Louvel, Guillaume Boulygina, Eugenia Sokolov, Alexey Nedoluzhko, Artem Lorenzen, Eline D Lopez, Patricio McDonald, H Gregory Scott, Eric Tikhonov, Alexei Stafford, Thomas W Alfarhan, Ahmed H Alquraishi, Saleh A Al-Rasheid, Khaled AS Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic 11826 2015-07-01 application/pdf https://escholarship.org/uc/item/0d70r11c unknown eScholarship, University of California qt0d70r11c https://escholarship.org/uc/item/0d70r11c public Scientific reports, vol 5, iss 1 Animals Ursidae DNA DNA Methylation Fossils Mammoths Genetics article 2015 ftcdlib 2023-02-06T18:41:26Z 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. Article in Journal/Newspaper eskimo* Saqqaq University of California: eScholarship |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Animals Ursidae DNA DNA Methylation Fossils Mammoths Genetics |
spellingShingle |
Animals Ursidae DNA DNA Methylation Fossils Mammoths Genetics Seguin-Orlando, Andaine Gamba, Cristina Sarkissian, Clio Der Ermini, Luca Louvel, Guillaume Boulygina, Eugenia Sokolov, Alexey Nedoluzhko, Artem Lorenzen, Eline D Lopez, Patricio McDonald, H Gregory Scott, Eric Tikhonov, Alexei Stafford, Thomas W Alfarhan, Ahmed H Alquraishi, Saleh A Al-Rasheid, Khaled AS Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic Pros and cons of methylation-based enrichment methods for ancient DNA. |
topic_facet |
Animals Ursidae DNA DNA Methylation Fossils Mammoths Genetics |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Seguin-Orlando, Andaine Gamba, Cristina Sarkissian, Clio Der Ermini, Luca Louvel, Guillaume Boulygina, Eugenia Sokolov, Alexey Nedoluzhko, Artem Lorenzen, Eline D Lopez, Patricio McDonald, H Gregory Scott, Eric Tikhonov, Alexei Stafford, Thomas W Alfarhan, Ahmed H Alquraishi, Saleh A Al-Rasheid, Khaled AS Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic |
author_facet |
Seguin-Orlando, Andaine Gamba, Cristina Sarkissian, Clio Der Ermini, Luca Louvel, Guillaume Boulygina, Eugenia Sokolov, Alexey Nedoluzhko, Artem Lorenzen, Eline D Lopez, Patricio McDonald, H Gregory Scott, Eric Tikhonov, Alexei Stafford, Thomas W Alfarhan, Ahmed H Alquraishi, Saleh A Al-Rasheid, Khaled AS Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic |
author_sort |
Seguin-Orlando, Andaine |
title |
Pros and cons of methylation-based enrichment methods for ancient DNA. |
title_short |
Pros and cons of methylation-based enrichment methods for ancient DNA. |
title_full |
Pros and cons of methylation-based enrichment methods for ancient DNA. |
title_fullStr |
Pros and cons of methylation-based enrichment methods for ancient DNA. |
title_full_unstemmed |
Pros and cons of methylation-based enrichment methods for ancient DNA. |
title_sort |
pros and cons of methylation-based enrichment methods for ancient dna. |
publisher |
eScholarship, University of California |
publishDate |
2015 |
url |
https://escholarship.org/uc/item/0d70r11c |
op_coverage |
11826 |
genre |
eskimo* Saqqaq |
genre_facet |
eskimo* Saqqaq |
op_source |
Scientific reports, vol 5, iss 1 |
op_relation |
qt0d70r11c https://escholarship.org/uc/item/0d70r11c |
op_rights |
public |
_version_ |
1766403400471150592 |