Historical RNA expression profiles from the extinct Tasmanian tiger

Area of Science:

• Paleogenomics
• Molecular Biology
• Evolutionary Biology

Background:

• Paleogenomics uses ancient DNA to study extinct species' evolution and ecology.
• DNA sequencing misses crucial transcriptional data like gene expression and cellular identity.
• Previous RNA extraction from ancient permafrost and historical skins was limited, with no attempts on extinct species.

Purpose of the Study:

• To extract, sequence, and analyze historical RNA from an extinct species (Tasmanian tiger).
• To obtain transcriptional profiles and gene expression dynamics from ancient specimens.
• To improve annotations and discover novel genetic elements in extinct animals.

Main Methods:

• RNA extraction and sequencing from a 130-year-old Tasmanian tiger specimen.
• Analysis of transcriptional profiles, metatranscriptomics, and RNA damage patterns.
• Genome-wide expression hotspot analysis and annotation refinement.

Main Results:

• Successful retrieval of historical RNA from Tasmanian tiger muscle and skin tissues.
• Transcriptional profiles resemble extant species, revealing anatomical features and confirming thylacine origin.
• Improved gene annotations, including microRNAs (from 62 to 325), and discovery of a thylacine-specific microRNA isoform.
• Detection of RNA viruses, suggesting potential for viral evolution studies.

Conclusions:

• This is the first successful extraction of transcriptional profiles from an extinct animal.
• Historical RNA analysis provides lost information on gene expression dynamics in extinct species.
• The method has significant implications for studying ancient RNA in museum collections and permafrost remains.