Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival.
While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relative...
Published in: | PLOS Biology |
---|---|
Main Authors: | , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science (PLoS)
2019
|
Subjects: | |
Online Access: | https://doi.org/10.1371/journal.pbio.3000166 https://doaj.org/article/4a497f7db82c42168caa7470879cac5c |
id |
ftdoajarticles:oai:doaj.org/article:4a497f7db82c42168caa7470879cac5c |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:4a497f7db82c42168caa7470879cac5c 2023-05-15T17:57:12+02:00 Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. Oliver Smith Glenn Dunshea Mikkel-Holger S Sinding Sergey Fedorov Mietje Germonpre Hervé Bocherens M T P Gilbert 2019-07-01T00:00:00Z https://doi.org/10.1371/journal.pbio.3000166 https://doaj.org/article/4a497f7db82c42168caa7470879cac5c EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pbio.3000166 https://doaj.org/toc/1544-9173 https://doaj.org/toc/1545-7885 1544-9173 1545-7885 doi:10.1371/journal.pbio.3000166 https://doaj.org/article/4a497f7db82c42168caa7470879cac5c PLoS Biology, Vol 17, Iss 7, p e3000166 (2019) Biology (General) QH301-705.5 article 2019 ftdoajarticles https://doi.org/10.1371/journal.pbio.3000166 2022-12-31T11:49:55Z While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data's authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology. Article in Journal/Newspaper permafrost Directory of Open Access Journals: DOAJ Articles PLOS Biology 17 7 e3000166 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Biology (General) QH301-705.5 |
spellingShingle |
Biology (General) QH301-705.5 Oliver Smith Glenn Dunshea Mikkel-Holger S Sinding Sergey Fedorov Mietje Germonpre Hervé Bocherens M T P Gilbert Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. |
topic_facet |
Biology (General) QH301-705.5 |
description |
While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data's authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology. |
format |
Article in Journal/Newspaper |
author |
Oliver Smith Glenn Dunshea Mikkel-Holger S Sinding Sergey Fedorov Mietje Germonpre Hervé Bocherens M T P Gilbert |
author_facet |
Oliver Smith Glenn Dunshea Mikkel-Holger S Sinding Sergey Fedorov Mietje Germonpre Hervé Bocherens M T P Gilbert |
author_sort |
Oliver Smith |
title |
Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. |
title_short |
Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. |
title_full |
Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. |
title_fullStr |
Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. |
title_full_unstemmed |
Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. |
title_sort |
ancient rna from late pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2019 |
url |
https://doi.org/10.1371/journal.pbio.3000166 https://doaj.org/article/4a497f7db82c42168caa7470879cac5c |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
PLoS Biology, Vol 17, Iss 7, p e3000166 (2019) |
op_relation |
https://doi.org/10.1371/journal.pbio.3000166 https://doaj.org/toc/1544-9173 https://doaj.org/toc/1545-7885 1544-9173 1545-7885 doi:10.1371/journal.pbio.3000166 https://doaj.org/article/4a497f7db82c42168caa7470879cac5c |
op_doi |
https://doi.org/10.1371/journal.pbio.3000166 |
container_title |
PLOS Biology |
container_volume |
17 |
container_issue |
7 |
container_start_page |
e3000166 |
_version_ |
1766165585170792448 |