Institut Jacques Monod

Duharcourt Lab VA

Programmed Genome Elimination

Sandra DUHARCOURT

Our work aims to understand the fundamental mechanisms governing chromosome structure and genetic stability in eukaryotes. We study a remarkable process of genome editing that occurs during development in the unicellular eukaryote Paramecium.

Keywords: epigenetics, transposable elements, non-coding RNA, chromatin, Polycomb, genome evolution, Paramecium

+33 (0)157278009     sandra.duharcourt(at)ijm.fr      @DuharcourtLab

Research

In Paramecium, at least one third of the germline genome is eliminated during development. This process involves the massive and reproducible elimination of repeated DNA sequences, such as transposable elements, and of 45,000 short non-coding sequences, scattered in the genome, relics of transposable elements. No conserved sequence motif that might serve as a specific recognition signal was identified among eliminated sequences. Understanding how such diverse sequences are recognized and excised remains challenging.

Current research aims to i) identify the eliminated sequences and describe their evolutionary trajectory, ii) elucidate the molecular mechanisms of programmed DNA elimination and iii) understand the possible functions associated with this massive genome reorganization.

The process involves small (s)RNA-directed heterochromatin formation and subsequent DNA excision and repair. sRNAs are produced from the germline genome during meiosis and guide the deposition of histone H3 post-translational epigenetic modifications (H3K9me3 and H3K27me3) onto sequences to be eliminated in the developing somatic nucleus, and specifically tether the DNA cleavage and repair machinery.

We demonstrated that the Paramecium histone methyltransferase Ezl1, a homolog of the mammalian PRC2 catalytic subunit, catalyzes H3K27me3 and H3K9me3 on TEs. We currently investigate how the Ezl1-associated complex is recruited to TEs, and how the histone H3 post-translational modifications trigger DNA cleavage and repair. We combine a large panel of molecular, cellular, high throughput sequencing, genetic and biochemical approaches to study the role of chromatin factors in the epigenetic control of DNA elimination.

Using an innovative flow cytometry approach to purify nuclei, we sequenced the genomes of nine Paramecium species for comparative genomics. These resources will allow us to elucidate the structure of Paramecium chromosomes, the evolutionary trajectories of eliminated sequences and their mechanisms of recognition and elimination.

Members

Group Leader:

Sandra DUHARCOURT
Tél : +33 (0)157278009
email : sandra.duharcourt (at) ijm.fr

 

Members :

Thomas BALAN PhD Student
Olivia CHARMANT Postdoc
Leticia KOCH LERNER Assistant professor
Louise ABBOU Engineer
Cristina RUBIO RAMON Research assistant
Marina GIOVANNETTI Master 2 Student
Maud LAGIER Master 2 Student
Estefania LETH

Selected Publications

All the publications since 2017

Publication 

2913254 MRLYRFX9 items 1 0 date desc 8637 https://www.ijm.fr/wp-content/plugins/zotpress/
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Charmant, O., Gruchota, J., Arnaiz, O., Zangarelli, C., Betermier, M., Nowak, K., Legros, V., Chevreux, G., Nowak, J., & Duharcourt, S. (2023). The nuclear PIWI-interacting protein Gtsf1 controls the selective degradation of small RNAs in Paramecium. bioRxiv. https://doi.org/10.1101/2023.09.19.558372
Miro-Pina, C., Arnaiz, O., Vanssay, A. de, Frapporti, A., Charmant, O., Humbert, A., Lhuillier-Akakpo, M., & Duharcourt, S. (2023). Non-catalytic function of PRC2 in the control of small RNA dynamics during programmed genome elimination in Paramecium. bioRxiv. https://doi.org/10.1101/2023.07.04.547679

 

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Balan, T., Lerner, L. K., Holoch, D., & Duharcourt, S. (2024). Small-RNA-guided histone modifications and somatic genome elimination in ciliates. WIREs RNA, 15(2), e1848. https://doi.org/10.1002/wrna.1848

 

Book chapter

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Duharcourt, S., & Sperling, L. (2018). The Challenges of Genome-Wide Studies in a Unicellular Eukaryote With Two Nuclear Genomes. Methods in Enzymology, 612, 101–126. https://doi.org/10.1016/bs.mie.2018.08.012

Theses

  • Thomas Balan 2021 – fellowship from Université Paris Cité (ED BioSPC)
  • Olivia Charmant 2019 – 2023 – fellowships from Université Paris Cité, FRM
  • Caridad Miro-Pina 2016-2020- fellowships from Université Paris Cité and Fondation ARC
  • Amandine Touzeau 2014-2018 – fellowships from Université Paris Cité and Fondation ARC
  • Andrea Frapporti 2012-2016 – fellowships from Université Paris Cité and FRM
  • Maoussi Lhuillier-Akakpo 2010-2014 fellowships from Sorbonne Université and FRM

Collaborations

Raphaël Margueron (Institut Curie, Paris, France)

Olivier Arnaiz (I2BC, Gif-sur-Yvette, France)

Slimane Ait-Si-Ali (EDC, Université Paris Cité, France)

Eric Meyer (IBENS, Paris, France)

Laurent Duret (LBBE, Lyon, France)

Mireille Bétermier (I2BC, Gif-sur-Yvette, France)

Chunlong Chen (Institut Curie, Paris, France)

Hadi Quesneville (INRAE, Versailles, France)

Karine Labadie/ Jean-Marc Aury (Génoscope, Evry, France)

Thomas Berendonk (TU, Dresden, Germany)

Ewa Przybòs/Natalia Sawka (ISEA PAS, Krakow, Poland)

Alexey Potekhin (SPBU, St. Petersburg, Russia)

Matthieu Defrance (ULB, Brussels, Belgium)

Julita Gruchota/Jacek Nowak (IBB, Warsaw, Poland)

GRANTS – FUNDING

ANR LaMarque 2018-2022                                           

ANR POLYCHROME 2019-2023

ANR SELECTION 2024-2027

 

         LabEx Who Am I? 2021-2023

 

    FRM labelled team 2022-2025

 

News

04/07/2023 – Sandra Duharcourt, election as a member of the EMBO community

04/04/2022 – Sandra Duharcourt, CNRS Silver Medal

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