Historical RNA expression profiles from the extinct Tasmanian tiger
(2023) In Genome Research 33(8). p.1299-1316- 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... (More)
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.
(Less)
- author
- organization
- publishing date
- 2023-08
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Genome Research
- volume
- 33
- issue
- 8
- pages
- 18 pages
- publisher
- Cold Spring Harbor Laboratory Press (CSHL)
- external identifiers
-
- pmid:37463752
- scopus:85173579499
- ISSN
- 1088-9051
- DOI
- 10.1101/gr.277663.123
- language
- English
- LU publication?
- yes
- id
- ca3544d0-b753-4739-8fe7-3a2b34ae501e
- date added to LUP
- 2023-12-20 10:56:29
- date last changed
- 2024-04-18 21:26:03
@article{ca3544d0-b753-4739-8fe7-3a2b34ae501e,
abstract = {{<p>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.</p>}},
author = {{Mármol-Sánchez, Emilio and Fromm, Bastian and Oskolkov, Nikolay and Pochon, Zoé and Kalogeropoulos, Panagiotis and Eriksson, Eli and Biryukova, Inna and Sekar, Vaishnovi and Ersmark, Erik and Andersson, Björn and Dalén, Love and Friedländer, Marc R.}},
issn = {{1088-9051}},
language = {{eng}},
number = {{8}},
pages = {{1299--1316}},
publisher = {{Cold Spring Harbor Laboratory Press (CSHL)}},
series = {{Genome Research}},
title = {{Historical RNA expression profiles from the extinct Tasmanian tiger}},
url = {{http://dx.doi.org/10.1101/gr.277663.123}},
doi = {{10.1101/gr.277663.123}},
volume = {{33}},
year = {{2023}},
}