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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ftgriffithuniv:oai:research-repository.griffith.edu.au:10072/172168 2023-05-15T16:06:51+02:00 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 D. Lopez, Patricio McDonald, H. Gregory Scott, Eric Tikhonov, Alexei Stafford Jr, Thomas W. Alfarhan, Ahmed H. Alquraishi, Saleh A. Al-Rasheid, Khaled A. S. Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic 2015 application/pdf http://hdl.handle.net/10072/172168 https://doi.org/10.1038/srep11826 English eng Nature Macmillan Scientific Reports http://creativecommons.org/licenses/by/4.0/ © The Author(s) 2015. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ CC-BY Biochemistry and Cell Biology not elsewhere classified Journal article 2015 ftgriffithuniv https://doi.org/10.1038/srep11826 2018-07-30T10:59:16Z 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. Full Text Article in Journal/Newspaper eskimo* Saqqaq Griffith University: Griffith Research Online Scientific Reports 5 1 |
institution |
Open Polar |
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Griffith University: Griffith Research Online |
op_collection_id |
ftgriffithuniv |
language |
English |
topic |
Biochemistry and Cell Biology not elsewhere classified |
spellingShingle |
Biochemistry and Cell Biology not elsewhere classified Seguin-Orlando, Andaine Gamba, Cristina Der Sarkissian, Clio Ermini, Luca Louvel, Guillaume Boulygina, Eugenia Sokolov, Alexey Nedoluzhko, Artem Lorenzen, Eline D. Lopez, Patricio McDonald, H. Gregory Scott, Eric Tikhonov, Alexei Stafford Jr, Thomas W. Alfarhan, Ahmed H. Alquraishi, Saleh A. Al-Rasheid, Khaled A. S. Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic Pros and cons of methylation-based enrichment methods for ancient DNA |
topic_facet |
Biochemistry and Cell Biology not elsewhere classified |
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. Full Text |
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 D. Lopez, Patricio McDonald, H. Gregory Scott, Eric Tikhonov, Alexei Stafford Jr, Thomas W. Alfarhan, Ahmed H. Alquraishi, Saleh A. Al-Rasheid, Khaled A. S. Shapiro, Beth Willerslev, Eske Prokhortchouk, Egor Orlando, Ludovic |
author_facet |
Seguin-Orlando, Andaine Gamba, Cristina Der Sarkissian, Clio Ermini, Luca Louvel, Guillaume Boulygina, Eugenia Sokolov, Alexey Nedoluzhko, Artem Lorenzen, Eline D. Lopez, Patricio McDonald, H. Gregory Scott, Eric Tikhonov, Alexei Stafford Jr, Thomas W. Alfarhan, Ahmed H. Alquraishi, Saleh A. Al-Rasheid, Khaled A. S. 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 |
Nature Macmillan |
publishDate |
2015 |
url |
http://hdl.handle.net/10072/172168 https://doi.org/10.1038/srep11826 |
genre |
eskimo* Saqqaq |
genre_facet |
eskimo* Saqqaq |
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Scientific Reports |
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http://creativecommons.org/licenses/by/4.0/ © The Author(s) 2015. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1038/srep11826 |
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Scientific Reports |
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5 |
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1766402872261476352 |