Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez1,2,
- Bastian Fromm1,3,
- Nikolay Oskolkov4,
- Zoé Pochon2,5,
- Panagiotis Kalogeropoulos1,
- Eli Eriksson1,
- Inna Biryukova1,
- Vaishnovi Sekar1,
- Erik Ersmark2,6,
- Björn Andersson7,
- Love Dalén2,6,8,9 and
- Marc R. Friedländer1,9
- 1Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
- 2Centre for Palaeogenetics, 106 91 Stockholm, Sweden;
- 3The Arctic University Museum of Norway, UiT - The Arctic University of Norway, 9006 Tromsø, Norway;
- 4Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 223 62 Lund, Sweden;
- 5Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden;
- 6Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden;
- 7Department of Cell and Molecular Biology (CMB), Karolinska Institute, 171 77 Stockholm, Sweden;
- 8Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
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↵9 These authors contributed equally to this work.
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.277663.123.
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Freely available online through the Genome Research Open Access option.
- Received January 5, 2023.
- Accepted June 27, 2023.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
