The analysis of ancient DNA (aDNA) has gained considerable momentum over the past decade, allowing the study of extinct or extant genomes from organisms that lived up to 2.5 million years ago. This has enabled the reconstruction of genomes and historical ancestry of multiple extinct renowned species such as Neanderthals, woolly mammoths, or Tasmanian tigers.
However, the characterization of animal historic/ancient RNA (aRNA) has essentially been ignored. We postulate the reason behind aRNA’s oblivion is a widely accepted preconception that all molecular biologists learn in their basic training: that RNA is an extremely fragile molecule. This is based on the reasoning that RNA is rapidly degraded by RNAses, making it virtually inexistent shortly after cell death if not immediately fixed, and certainly not durable through long periods of time.
We believe this to be fairly reductionist. A handful of studies have determined flash-frozen historic/ancient animal remains and formalin-fixed paraffin-embedded (FFPE) tissues as a promising source of aRNA. Other common preservation methods in museum collections – e.g. desiccation or liquid ethanol fixation – are still mainly unexplored, and hold similar ability to inactivate RNAses.
The key questions therefore are:
- Are these preservation methods generalizable conditions in which animal’s RNA molecules could survive?
- Can we define the gold-standard laboratory and computational methods allowing ancient RNA research to finally emerge as a consolidated field?
In this Bachelor/Master's thesis project, you will have the chance to work hands-on in the methodological development of new techniques for preparing, extracting and sequencing ancient RNA molecules from museum-preserved and ancient tissues from different animal sources. Working on a laboratory environment tailored for managing ancient samples, you will develop an exciting cutting-edge project in a research field barely explored so far. Besides, you will also have the chance to explore new approaches for the statistical and bioinformatic analysis of the sequencing data generated during the laboratory work.
You will gain experience in:
- aDNA and aRNA laboratory protocols
- Bioinformatic processing
- Data analysis in R, writing, and data visualization
What we are looking for:
- Interest in laboratory methods development
- Curiosity and practical problem-solving
- Willing to learn bioinformatics applied to paleogenetics
Recommended:
- Experience in molecular biology laboratory techniques (DNA & RNA preferred)
- Basic knowledge of UNIX and R (not a must).
Timeline:
Starting date and timeline is flexible and negotiable. The project is expected to start around May 2026, or soon later depending on the student´s availability and Bachelor/MSc schedules.
We will be assessing candidates during March and April as they show interest and contacting them back if we find a fit.
Please do not hesitate to contact for further inquiries and additional information.
For international Bachelor/MSc students and PhD candidates, applications through Erasmus+ or any other dedicated funders for short research stays are also welcome!!
Contact:
Dr. Emilio Mármol Sánchez (< email usunięty ze względów bezpieczeństwa >)
Prof. Tom Gilbert (< email usunięty ze względów bezpieczeństwa >)
Relevant literature:
- Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Dehasque M, Bozlak E, Brown K, Aslanzadeh M, van der Valk T, Chacón-Duque CJ, Kalogeropoulos P, Biryukova I, Heintzman PD, Furugård C, Plotnikov V, Protopopov A, Andersson B, Ersmark E, Peterson KJ, Friedländer MR, Da expression profiles from the extinct woolly mammoth. Cell 2025; 189:52–69.e22.
- Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Kalogeropoulos P, Eriksson E, Biryukova I, Sekar V, Ersmark E, Andersson B, Dalén L, Friedländer MR. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Research 2023; 3:1299-1316.
- Fromm B et al. Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene. RNA. 2021; 27:324–34.
- Smith O et al. Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transtome survival. PLoS Biol. 2019; 17:e3000166.