Description du sujet de thèse

Our laboratory is exploring the mechanisms and evolutionary origins of programmed DNA elimination, which has been observed in various invertebrate and vertebrate species 1. This process occurs during embryogenesis and, in some cases, leads to the fragmentation and partial elimination of all chromosomes in all somatic cells at every generation. Consequently, animals possess two genomes: an intact one in the germline and a reduced one in the soma.
Our laboratory has identified programmed DNA elimination in a genetically tractable nematode species, offering the possibility to explore this process, which has remained mysterious since its discovery 150 years ago, due to a lack of model species 2,3. The candidate will use a combination of genetic tools to identify the molecular machinery responsible for chromosome fragmentation in one species. Secondly, they will explore the evolution of this molecular complex (or single nuclease) across nematode species to understand its origin.
In parallel, they will analyse the dynamics of gains and losses of the motif sequence found at chromosome breakpoints using our collection of well-assembled genomes at different evolutionary scales (haplotypes, strains, and species) via bioinformatic approaches.

The candidate should have past experience in bioinformatics and a strong background in experimental work (ideally basic molecular biology and cytology/imaging). Experience with nematodes would be advantageous but is not mandatory.

1. Dedukh, D., and Krasikova, A. (2022). Delete and survive: strategies of programmed genetic material elimination in eukaryotes. Biol Rev Camb Philos Soc 97, 195–216. https://doi.org/10.1111/brv.12796.
2. Rey, C., Launay, C., Wenger, E., and Delattre, M. (2022). Programmed-DNA Elimination in the free-living nematodes Mesorhabditis. bioRxiv, 2022.03.19.484980. https://doi.org/10.1101/2022.03.19.484980.
3. Launay, C., Wenger, E., Letcher, B., and Delattre, M. (2025). Programmed DNA Elimination is widespread in free-living Rhabditidae nematodes. Preprint at bioRxiv, https://doi.org/10.1101/2025.08.21.671558 https://doi.org/10.1101/2025.08.21.671558.

Contexte de travail

Our institute (LBMC) is located on the Monod site of the École Normale Supérieure de Lyon (ENS), just south of Lyon's city center (France). ENS offers a rich interdisciplinary environment, bringing together 30 research units spanning fields from archaeology to quantum physics. This project is part of an interdisciplinary research program.
The successful candidate will join a collaborative team where bioinformaticians and experimentalists work closely together, ensuring strong support for every stage of the project.
In addition, the institute offers access to state-of-the-art facilities and a dynamic scientific ecosystem supporting both experimental and computational research. In particular:
• A high-quality imaging platform
• A dedicated biocomputing hub that guarantees reliable data storage, management, and advanced analytical capacity.

Contraintes et risques

none

Informations complémentaires

none