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Home > Departments > Genome Biology > Mireille BETERMIER : Programmed genome rearrangements

Mireille BETERMIER : Group Presentation

In numerous eukaryotes, the developmentally programmed elimination of germline DNA sequences drives the plasticity of the somatic genome. Using the ciliate Paramecium tetraurelia as a unicellular model organism, the Bétermier lab studies how transposable elements and cellular DNA repair pathways contribute to programmed genome rearrangements and their epigenetic control.

Transposons and their host genomes

DNA transposons move around host genomes through the action of their cognate transposases. Transposon mobility drives the plasticity of host genomes by introducing mutations, modifying the regulation of gene expression or triggering ectopic recombination. Host organisms have developed various strategies to cope with transposon invasion, such as silencing through RNA interference, DNA methylation or embedment into heterochromatin, or transposon degeneration through accumulation of point mutations and deletions. DNA transposons have been classified in more than ten distinct families according to the structure of their respective transposases, the terminal inverted repeats (TIR) present at their ends and the details of their transposition mechanisms. Transposases usually bind specifically to transposon TIRs and cleave DNA to initiate transposition. During evolution, some transposase genes have been exapted by the host to become cellular genes. Except for a few of examples, however, the cellular function of “domesticated” transposases has remained elusive.

Paramecium: a model unicellular microorganism

Because of its unique nuclear dimorphism, the ciliate Paramecium has become an extraordinary unicellular model to study the impact of transposable elements on genome dynamics. As in other ciliates, two distinct nuclei coexist in Paramecium. The transcriptionally silent diploid micronucleus (MIC) contains the 100-Mbp germline genome that is transmitted to sexual progeny following meiosis. The polyploid somatic macronucleus (MAC) is responsible for gene transcription and essential for cell survival. At each sexual cycle, the parental MAC is destroyed and a new MAC differentiates from a copy of the zygotic nucleus, which contains the germline genome.

In the developing new MAC, the genome undergoes multiple rounds of endoreplication. Concomitantly, massive programmed genome rearrangements lead to elimination of 25 to 30 % of germline: (i) repeated sequences (transposons, minisatellites) are eliminated in association with chromosome fragmentation or heterogeneous internal deletions; (ii) 45,000 short, single copy, noncoding sequences scattered throughout the genome (IES, or internal eliminated sequences) are excised precisely to reconstitute functional open reading frames. At least a fraction of Paramecium IES are degenerated transposons related to the Tc/mariner family. However, no conserved TIR could be found at IES ends, and how these elements are specifically recognized for elimination remains an open question.

We identified recently several key actors of IES excision. PiggyMac, a potentially active domesticated transposase from the piggyBac family, is essential for the introduction of programmed DNA double-strand breaks (DSB) at IES ends. The classical nonhomologous end-joining (C-NHEJ) DSB repair pathway, involving a development-specific Ku70/Ku80 heterodimer and the Ligase IV/Xrcc4 complex, mediates highly precise repair of IES excision sites and allows the assembly of functional genes in the MAC. We recently demonstrated that DNA cleavage at IES ends is entirely dependent upon the presence of Ku proteins, which form a complex with PiggyMac in heterologous cell extracts. We are currently using molecular, biochemical and cellular approaches combined with reverse genetics and next-generation sequencing to study the PiggyMac complex and the mechanism of IES recognition within chromatin.

Keywords:

Ciliates, Paramecium, transposons, piggyBac, domesticated transposase, programmed genome rearrangements, epigenetics, DNA repair, NHEJ, double-strand breaks

Contacts


BETERMIER Mireille [Senior Researcher - CNRS]
Department of genomes biology [Leader]
Programmed genome rearrangements [Leader]
01 69 82 31 64 Gif - Bât 26


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