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

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.

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

Cristina RUBIO RAMON, Research assistant

Marina GIOVANNETTI, Master 2 Student

Maud LAGIER, Master 2 Student

Mélodie RICHARD, Master 1 Student

Publication 

Gout, J.-F., Hao, Y., Johri, P., Arnaiz, O., Doak, T. G., Bhullar, S., Couloux, A., Guérin, F., Malinsky, S., Potekhin, A., Sawka, N., Sperling, L., Labadie, K., Meyer, E., Duharcourt, S., & Lynch, M. (2023). Dynamics of Gene Loss following Ancient Whole-Genome Duplication in the Cryptic Paramecium Complex. Molecular Biology and Evolution, 40(5), msad107. https://doi.org/10.1093/molbev/msad107
Hardy, A., Duharcourt, S., & Defrance, M. (2023). DNA Modification Patterns Filtering and Analysis Using DNAModAnnot. Methods in Molecular Biology (Clifton, N.J.), 2624, 87–114. https://doi.org/10.1007/978-1-0716-2962-8_7
Miró-Pina, C., Charmant, O., Kawaguchi, T., Holoch, D., Michaud, A., Cohen, I., Humbert, A., Jaszczyszyn, Y., Chevreux, G., Del Maestro, L., Ait-Si-Ali, S., Arnaiz, O., Margueron, R., & Duharcourt, S. (2022). Paramecium Polycomb repressive complex 2 physically interacts with the small RNA-binding PIWI protein to repress transposable elements. Developmental Cell, 57(8), 1037-1052.e8. https://doi.org/10.1016/j.devcel.2022.03.014
Gnan, S., Matelot, M., Weiman, M., Arnaiz, O., Guérin, F., Sperling, L., Bétermier, M., Thermes, C., Chen, C.-L., & Duharcourt, S. (2022). GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium. Genome Research, 32(4), 699–709. https://doi.org/10.1101/gr.276125.121
Déléris, A., Berger, F., & Duharcourt, S. (2021). Role of Polycomb in the control of transposable elements. Trends in Genetics: TIG, 37(10), 882–889. https://doi.org/10.1016/j.tig.2021.06.003
Sellis, D., Guérin, F., Arnaiz, O., Pett, W., Lerat, E., Boggetto, N., Krenek, S., Berendonk, T., Couloux, A., Aury, J.-M., Labadie, K., Malinsky, S., Bhullar, S., Meyer, E., Sperling, L., Duret, L., & Duharcourt, S. (2021). Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes. PLoS Biology, 19(7), e3001309. https://doi.org/10.1371/journal.pbio.3001309
Hardy, A., Matelot, M., Touzeau, A., Klopp, C., Lopez-Roques, C., Duharcourt, S., & Defrance, M. (2021). DNAModAnnot: a R toolbox for DNA modification filtering and annotation. Bioinformatics (Oxford, England), btab032. https://doi.org/10.1093/bioinformatics/btab032
Grentzinger, T., Oberlin, S., Schott, G., Handler, D., Svozil, J., Barragan-Borrero, V., Humbert, A., Duharcourt, S., Brennecke, J., & Voinnet, O. (2020). A universal method for the rapid isolation of all known classes of functional silencing small RNAs. Nucleic Acids Research, 48(14), e79. https://doi.org/10.1093/nar/gkaa472
de Vanssay, A., Touzeau, A., Arnaiz, O., Frapporti, A., Phipps, J., & Duharcourt, S. (2020). The Paramecium histone chaperone Spt16-1 is required for Pgm endonuclease function in programmed genome rearrangements. PLoS Genetics, 16(7), e1008949. https://doi.org/10.1371/journal.pgen.1008949
Frapporti, A., Miró Pina, C., Arnaiz, O., Holoch, D., Kawaguchi, T., Humbert, A., Eleftheriou, E., Lombard, B., Loew, D., Sperling, L., Guitot, K., Margueron, R., & Duharcourt, S. (2019). The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium. Nature Communications, 10(1), 2710. https://doi.org/10.1038/s41467-019-10648-5
Arnaiz, O., Van Dijk, E., Bétermier, M., Lhuillier-Akakpo, M., de Vanssay, A., Duharcourt, S., Sallet, E., Gouzy, J., & Sperling, L. (2017). Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression. BMC Genomics, 18(1), 483. https://doi.org/10.1186/s12864-017-3887-z
Guérin, F., Arnaiz, O., Boggetto, N., Denby Wilkes, C., Meyer, E., Sperling, L., & Duharcourt, S. (2017). Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements. BMC Genomics, 18(1), 327. https://doi.org/10.1186/s12864-017-3713-7

 

Preprint

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

 

Book chapter

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
  • 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 2012-2016fellowships from Université Paris Cité and FRM
  • Maoussi Lhuillier-Akakpo 2010-2014 fellowships from Sorbonne Université and FRM

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)

ANR LaMarque 2018-2022                                           

ANR POLYCHROME 2019-2023

ANR SELECTION 2024-2027

 

         LabEx Who Am I? 2021-2023

 

    FRM labelled team 2022-2025

 

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

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