Programmed genome

Chromosome rearrangements can compromise genome integrity. Programmed rearrangements nevertheless take place during physiological processes, such as antibody gene assembly in immune cells. Using the ciliate Paramecium tetraurelia as a model, we study the contribution of transposable elements and DNA double-strand break repair pathways to the developmentally programmed elimination of germline DNA.

Paramecium as a model

Paramecium is a unicellular eukaryote belonging to the phylum of ciliates. Like other ciliates, it harbors two functionally distinct nuclei inside the same cytoplasm. The transcriptionally silent diploid micronucleus (MIC) contains the germline genome that is transmitted to sexual progeny following meiosis. The polyploid somatic macronucleus (MAC), responsible for gene transcription, contains a rearranged version of the germline genome. At each sexual cycle, the parental MAC is destroyed and a new MAC differentiates from a copy of the MIC-derived zygotic nucleus, a process that includes the elimination of a substantial fraction of germline DNA. More about Paramecium

Programmed genome rearrangements

We study programmed genome rearrangements in a model species: Paramecium tetraurelia, which carries a ~100 Mb germline genome. During MAC development, the genome undergoes multiple rounds of endoreplication. Concomitantly, massive programmed genome rearrangements eliminate at least 25 to 30% of germline DNA. These rearrangements include (i) removal of repeated sequences (transposons, minisatellites), leading to chromosome fragmentation or heterogeneous internal deletions and (ii) excision of ~ 45,000 short, single copy and noncoding sequences scattered throughout the genome (IES, or internal eliminated sequences).  Precise IES excision is necessary to reconstitute functional open reading frames. At least a fraction of Paramecium IESs are the degenerate remnants of transposons related to the Tc/mariner family.




Group Leader

Research Director - CNRS


Research Director - CEA

Olivier ARNAIZ

Engineer - CNRS


Postdoctoral Researcher


Researcher - CNRS

Vinciane REGNIER

Assistant Professor
Université de Paris


Emeritus Researcher
Director - CNRS

Valerio VITALI

Postdoctoral Researcher


Assistant Engineer CNRS

Latest publications

The unusual structure of the PiggyMac cysteine-rich domain reveals zinc finger diversity in PiggyBac-related transposases. Guérineau M, Bessa L, Moriau S, Lescop E, Bontems F, Mathy N, Guittet E, Bischerour J, Bétermier M, Morellet N. Mob DNA. 2021 Apr 29;12(1):12. doi: 10.1186/s13100-021-00240-4. PMID: 33926516


Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes. Sellis D, Guérin F, Arnaiz O, Pett W, Lerat E, Boggetto N, Krenek S, Berendonk T, Couloux A, Aury JM, Labadie K, Malinsky S, Bhullar S, Meyer E, Sperling L, Duret L, Duharcourt S. PLoS Biol. 2021 Jul 29;19(7):e3001309. doi: 10.1371/journal.pbio.3001309. eCollection 2021 Jul. PMID: 34324490

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External funding

ANR LaMarque (2018-2023)


Principal Investigator: Mireille Bétermier




Principal Investigator: Mireille Bétermier



Principal Investigator: Olivier Arnaiz

Equipe labellisée FRM (2021-2025)

Principal Investigator: Mireille Bétermier

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