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...
Published in: | Scientific Reports |
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Online Access: | https://curis.ku.dk/portal/da/publications/pros-and-cons-of-methylationbased-enrichment-methods-for-ancient-dna(ee20884d-c4c1-4c30-9e8b-31500f99428e).html https://doi.org/10.1038/srep11826 https://curis.ku.dk/ws/files/154747316/Seguin_Orlando_2015_Pros_and_cons.pdf |
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ftcopenhagenunip:oai:pure.atira.dk:publications/ee20884d-c4c1-4c30-9e8b-31500f99428e 2024-05-19T07:39:47+00:00 Pros and cons of methylation-based enrichment methods for ancient DNA Seguin-Orlando, Andaine Gamba, Cristina Der Sarkissian, Clio Ermini, Luca Louvel, Guillaume Boulygina, Eugenia Sokolov, Alexey Nedoluzhko, Artem Lorenzen, Eline Lopez, Patricio McDonald, H. Gregory Scott, Eric Tikhonov, Alexei Stafford jr., Thomas Alfarhan, Ahmed H. Alquraishi, Saleh A. Al-Rasheid, Khaled A. S. Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic Antoine Alexandre 2015 application/pdf https://curis.ku.dk/portal/da/publications/pros-and-cons-of-methylationbased-enrichment-methods-for-ancient-dna(ee20884d-c4c1-4c30-9e8b-31500f99428e).html https://doi.org/10.1038/srep11826 https://curis.ku.dk/ws/files/154747316/Seguin_Orlando_2015_Pros_and_cons.pdf eng eng info:eu-repo/semantics/openAccess Seguin-Orlando , A , Gamba , C , Der Sarkissian , C , Ermini , L , Louvel , G , Boulygina , E , Sokolov , A , Nedoluzhko , A , Lorenzen , E , Lopez , P , McDonald , H G , Scott , E , Tikhonov , A , Stafford jr. , T , Alfarhan , A H , Alquraishi , S A , Al-Rasheid , K A S , Shapiro , B , Willerslev , E , Prokhortchouk , E & Orlando , L A A 2015 , ' Pros and cons of methylation-based enrichment methods for ancient DNA ' , Scientific Reports , vol. 5 , 11826 . https://doi.org/10.1038/srep11826 article 2015 ftcopenhagenunip https://doi.org/10.1038/srep11826 2024-04-25T00:45:02Z 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 Copenhagen: Research Scientific Reports 5 1 |
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Open Polar |
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University of Copenhagen: Research |
op_collection_id |
ftcopenhagenunip |
language |
English |
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 Der Sarkissian, Clio Ermini, Luca Louvel, Guillaume Boulygina, Eugenia Sokolov, Alexey Nedoluzhko, Artem Lorenzen, Eline Lopez, Patricio McDonald, H. Gregory Scott, Eric Tikhonov, Alexei Stafford jr., Thomas Alfarhan, Ahmed H. Alquraishi, Saleh A. Al-Rasheid, Khaled A. S. Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic Antoine Alexandre |
spellingShingle |
Seguin-Orlando, Andaine Gamba, Cristina Der Sarkissian, Clio Ermini, Luca Louvel, Guillaume Boulygina, Eugenia Sokolov, Alexey Nedoluzhko, Artem Lorenzen, Eline Lopez, Patricio McDonald, H. Gregory Scott, Eric Tikhonov, Alexei Stafford jr., Thomas Alfarhan, Ahmed H. Alquraishi, Saleh A. Al-Rasheid, Khaled A. S. Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic Antoine Alexandre Pros and cons of methylation-based enrichment methods for ancient DNA |
author_facet |
Seguin-Orlando, Andaine Gamba, Cristina Der Sarkissian, Clio Ermini, Luca Louvel, Guillaume Boulygina, Eugenia Sokolov, Alexey Nedoluzhko, Artem Lorenzen, Eline Lopez, Patricio McDonald, H. Gregory Scott, Eric Tikhonov, Alexei Stafford jr., Thomas Alfarhan, Ahmed H. Alquraishi, Saleh A. Al-Rasheid, Khaled A. S. Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic Antoine Alexandre |
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 |
publishDate |
2015 |
url |
https://curis.ku.dk/portal/da/publications/pros-and-cons-of-methylationbased-enrichment-methods-for-ancient-dna(ee20884d-c4c1-4c30-9e8b-31500f99428e).html https://doi.org/10.1038/srep11826 https://curis.ku.dk/ws/files/154747316/Seguin_Orlando_2015_Pros_and_cons.pdf |
genre |
eskimo* Saqqaq |
genre_facet |
eskimo* Saqqaq |
op_source |
Seguin-Orlando , A , Gamba , C , Der Sarkissian , C , Ermini , L , Louvel , G , Boulygina , E , Sokolov , A , Nedoluzhko , A , Lorenzen , E , Lopez , P , McDonald , H G , Scott , E , Tikhonov , A , Stafford jr. , T , Alfarhan , A H , Alquraishi , S A , Al-Rasheid , K A S , Shapiro , B , Willerslev , E , Prokhortchouk , E & Orlando , L A A 2015 , ' Pros and cons of methylation-based enrichment methods for ancient DNA ' , Scientific Reports , vol. 5 , 11826 . https://doi.org/10.1038/srep11826 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1038/srep11826 |
container_title |
Scientific Reports |
container_volume |
5 |
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1 |
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1799479372715917312 |