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Historical RNA expr...
Historical RNA expression profiles from the extinct Tasmanian tiger
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- Mármol-Sánchez, Emilio (author)
- Stockholm University,Stockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för molekylär biovetenskap, Wenner-Grens institut,Centre for Palaeogenetics, Sweden
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- Fromm, Bastian (author)
- Stockholm University,Stockholms universitet,Institutionen för molekylär biovetenskap, Wenner-Grens institut,Science for Life Laboratory (SciLifeLab),UiT - The Arctic University of Norway, Norway,UiT The Arctic University of Norway, Tromsø
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- Oskolkov, Nikolay (author)
- Lund University,Lunds universitet,Molekylär cellbiologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Bioinformatik,Forskargrupper vid Lunds universitet,LTH profilområde: Teknik för hälsa,LTH profilområden,Lunds Tekniska Högskola,Molecular Cell Biology,Department of Biology,Faculty of Science,Bioinformatics,Lund University Research Groups,LTH Profile Area: Engineering Health,LTH Profile areas,Faculty of Engineering, LTH
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- Pochon, Zoé (author)
- Stockholm University,Stockholms universitet,Institutionen för arkeologi och antikens kultur,Centre for Palaeogenetics, Sweden
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- Kalogeropoulos, Panagiotis (author)
- Stockholm University,Stockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för molekylär biovetenskap, Wenner-Grens institut
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- Eriksson, Eli (author)
- Stockholm University,Stockholms universitet,Institutionen för molekylär biovetenskap, Wenner-Grens institut,Science for Life Laboratory (SciLifeLab)
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- Biryukova, Inna (author)
- Stockholm University,Stockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för molekylär biovetenskap, Wenner-Grens institut
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- Sekar, Vaishnovi (author)
- Stockholm University,Stockholms universitet,Institutionen för molekylär biovetenskap, Wenner-Grens institut,Science for Life Laboratory (SciLifeLab)
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- Ersmark, Erik (author)
- Swedish Museum of Natural History
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- Andersson, Björn (author)
- Karolinska Institute,Karolinska Institutet
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- Dalén, Love, 1980- (author)
- Stockholm University,Swedish Museum of Natural History,Stockholms universitet,Zoologiska institutionen,Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden
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- Friedländer, Marc R. (author)
- Stockholm University,Stockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för molekylär biovetenskap, Wenner-Grens institut
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(creator_code:org_t)
- 2023
- 2023
- English.
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In: Genome Research. - 1088-9051 .- 1549-5469. ; 33:8, s. 1299-1316
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Abstract
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- 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 protein-coding 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Mármol-Sánchez, ...
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Fromm, Bastian
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Oskolkov, Nikola ...
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Pochon, Zoé
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Kalogeropoulos, ...
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Eriksson, Eli
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show more...
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Biryukova, Inna
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Sekar, Vaishnovi
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Ersmark, Erik
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Andersson, Björn
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Dalén, Love, 198 ...
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Friedländer, Mar ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Evolutionary Bio ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Genetics
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
- Articles in the publication
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Genome Research
- By the university
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Stockholm University
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Karolinska Institutet
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Lund University