Historical RNA expression profiles from the extinct Tasmanian tiger
Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcrip...
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ftunivtroemsoe:oai:munin.uit.no:10037/32346 2024-02-04T10:03:51+01:00 Historical RNA expression profiles from the extinct Tasmanian tiger Mármol-Sánchez, Emilio Fromm, Bastian Oskolkov, Nikolay Pochon, Zoé Kalogeropoulos, Panagiotis Eriksson, Eli Biryukova, Inna Sekar, Vaishnovi Ersmark, Erik Andersson, Björn Dalén, Love Friedländer, Marc R. 2023-07-18 https://hdl.handle.net/10037/32346 https://doi.org/10.1101/gr.277663.123 eng eng Cold Spring Harbor Laboratory Press Genome Research Mármol-Sánchez, Fromm, Oskolkov, Pochon, Kalogeropoulos, Eriksson, Biryukova, Sekar, Ersmark, Andersson, Dalén, Friedländer. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Research. 2023;33(8):1299-1316 FRIDAID 2193295 doi:10.1101/gr.277663.123 1088-9051 1549-5469 https://hdl.handle.net/10037/32346 Attribution 4.0 International (CC BY 4.0) openAccess Copyright 2023 The Author(s) https://creativecommons.org/licenses/by/4.0 Journal article Tidsskriftartikkel Peer reviewed publishedVersion 2023 ftunivtroemsoe https://doi.org/10.1101/gr.277663.123 2024-01-11T00:08:07Z Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve proteincoding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains. Article in Journal/Newspaper permafrost University of Tromsø: Munin Open Research Archive Genome Research 33 8 1299 1316 |
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University of Tromsø: Munin Open Research Archive |
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ftunivtroemsoe |
language |
English |
description |
Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve proteincoding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains. |
format |
Article in Journal/Newspaper |
author |
Mármol-Sánchez, Emilio Fromm, Bastian Oskolkov, Nikolay Pochon, Zoé Kalogeropoulos, Panagiotis Eriksson, Eli Biryukova, Inna Sekar, Vaishnovi Ersmark, Erik Andersson, Björn Dalén, Love Friedländer, Marc R. |
spellingShingle |
Mármol-Sánchez, Emilio Fromm, Bastian Oskolkov, Nikolay Pochon, Zoé Kalogeropoulos, Panagiotis Eriksson, Eli Biryukova, Inna Sekar, Vaishnovi Ersmark, Erik Andersson, Björn Dalén, Love Friedländer, Marc R. Historical RNA expression profiles from the extinct Tasmanian tiger |
author_facet |
Mármol-Sánchez, Emilio Fromm, Bastian Oskolkov, Nikolay Pochon, Zoé Kalogeropoulos, Panagiotis Eriksson, Eli Biryukova, Inna Sekar, Vaishnovi Ersmark, Erik Andersson, Björn Dalén, Love Friedländer, Marc R. |
author_sort |
Mármol-Sánchez, Emilio |
title |
Historical RNA expression profiles from the extinct Tasmanian tiger |
title_short |
Historical RNA expression profiles from the extinct Tasmanian tiger |
title_full |
Historical RNA expression profiles from the extinct Tasmanian tiger |
title_fullStr |
Historical RNA expression profiles from the extinct Tasmanian tiger |
title_full_unstemmed |
Historical RNA expression profiles from the extinct Tasmanian tiger |
title_sort |
historical rna expression profiles from the extinct tasmanian tiger |
publisher |
Cold Spring Harbor Laboratory Press |
publishDate |
2023 |
url |
https://hdl.handle.net/10037/32346 https://doi.org/10.1101/gr.277663.123 |
genre |
permafrost |
genre_facet |
permafrost |
op_relation |
Genome Research Mármol-Sánchez, Fromm, Oskolkov, Pochon, Kalogeropoulos, Eriksson, Biryukova, Sekar, Ersmark, Andersson, Dalén, Friedländer. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Research. 2023;33(8):1299-1316 FRIDAID 2193295 doi:10.1101/gr.277663.123 1088-9051 1549-5469 https://hdl.handle.net/10037/32346 |
op_rights |
Attribution 4.0 International (CC BY 4.0) openAccess Copyright 2023 The Author(s) https://creativecommons.org/licenses/by/4.0 |
op_doi |
https://doi.org/10.1101/gr.277663.123 |
container_title |
Genome Research |
container_volume |
33 |
container_issue |
8 |
container_start_page |
1299 |
op_container_end_page |
1316 |
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1789971633566384128 |