Thèse en cours

Variation génétique naturelle dans des phénomènes non génétiques multigénérationnels chez Caenorhabditis elegans

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Auteur / Autrice : Marie Saglio
Direction : Marie-Anne Felix
Type : Projet de thèse
Discipline(s) : Génétique et génomique
Date : Inscription en doctorat le 01/10/2018
Etablissement(s) : Université Paris sciences et lettres
Ecole(s) doctorale(s) : École doctorale Complexité du vivant (Paris)
Partenaire(s) de recherche : Laboratoire : Institut de biologie de l'École normale supérieure (Paris ; 2010-....)
Equipe de recherche : Évolution des Caenorhabditis
établissement opérateur d'inscription : École normale supérieure (Paris ; 1985-....)

Mots clés

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While heredity mostly relies on DNA sequence, other molecular and cellular features are heritable across generations. This non-DNA sequence-based memory could be of importance for adaptation of organisms to a varying environment. Here I test whether and how such non-genetic inheritance systems are modulated by natural genetic variation. I use two experimental paradigms: 1) the mortal germline phenotype and 2) the memory of RNA interference (RNAi). The mortal germline (Mrt) phenotype is a progressive onset of sterility over multiple generations (Ahmed and Hodgkin, 2000; Xue and Leibler, 2016). Temperature-sensitive Mrt mutations are known to affect small RNA pathways, histone methylation and thereby multigenerational inheritance (Buckley et al., 2012; Katz et al., 2009; Spracklin et al., 2017; Xiao et al., 2011). In the second paradigm, inheritance of RNA interference (RNAi) is directly assayed over several generations once the initial trigger is removed (Alcazar et al., 2008; Grishok, 2000; Priyadarshini et al., 2022; Vastenhouw et al., 2006). The laboratory previously showed that some C. elegans natural isolates display a temperature-sensitive Mrt phenotype (Frézal et al., 2018). Using recombinants between two isolates of contrasted Mrt phenotype, they identified a causal polymorphism in the set-24 gene. The set-24 Mrt allele turned out to be a rare allele. Aiming at identifying polymorphisms underlying the Mrt phenotype at the species level, I performed a genome-wide association study with about 100 wild isolates. A strong association on chromosome III was found. Introgressions of chromosome III from the strong Mrt isolate JU775 in a non-Mrt genetic background confirmed the association. These results show that a genetic variant underlying the multigenerational phenotype is found at intermediate frequency at the species scale. As the Mrt phenotype observed in the laboratory leads to the sterility of the lineage, it is likely suppressed in nature, by temperature variation or potentially other interactions. We indeed found that naturally associated bacteria or infection by microsporidia strongly suppress the Mrt phenotype. Thus, the Mrt phenotype is likely revealed in laboratory conditions, thereby providing an experimental handle on natural variation in transgenerational inheritance pathways. Importantly, we also reveal a positive, condition-dependent effect of an intestinal "pathogen", affecting the C. elegans germline. In addition to the Mrt phenotype, I turned to directly assay the memory of RNA interference. We independently introduced two different germline-expressed GFP transgenes in genetically divergent wild isolates. I followed the silencing memory of an RNAi trigger provided in the first generation and show that C. elegans wild isolates differ in the number of generations of silencing. While some isolates consistently show a strong memory for multiple generations in the absence of the RNAi trigger (e.g. EG4725), others have a very short memory (e.g. JU775), or no memory at all. Some strains also show an intermediate memory such as the N2 reference strain. Overall, I show that multigenerational memory is modulated by natural genetic variation in C. elegans. REFERENCE Ahmed, S., Hodgkin, J., 2000. MRT-2 checkpoint protein is required for germline immortality and telomere replication in C. elegans. Nature 403, 159–164. Alcazar, R.M., Lin, R., Fire, A.Z., 2008. Transmission Dynamics of Heritable Silencing Induced by Double-Stranded RNA in Caenorhabditis elegans. Genetics 180, 1275–1288. Aljohani, M.D., El Mouridi, S., Priyadarshini, M., Vargas-Velazquez, A.M., Frøkjær-Jensen, C., 2020. Engineering rules that minimize germline silencing of transgenes in simple extrachromosomal arrays in C. elegans. Nat Commun 11, 6300. Ashe, A., Sapetschnig, A., Weick, E.-M., Mitchell, J., Bagijn, M.P., Cording, A.C., Doebley, A.-L., Goldstein, L.D., Lehrbach, N.J., Le Pen, J., Pintacuda, G., Sakaguchi, A., Sarkies, P., Ahmed, S., Miska, E.A., 2012. piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans. Cell 150, 88–99. Buckley, B.A., Burkhart, K.B., Gu, S.G., Spracklin, G., Kershner, A., Fritz, H., Kimble, J., Fire, A., Kennedy, S., 2012. A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality. Nature 489, 447–451. Frézal, L., Demoinet, E., Braendle, C., Miska, E., Félix, M.-A., 2018. Natural Genetic Variation in a Multigenerational Phenotype in C. elegans. Current Biology 28, 2588-2596.e8. Grishok, A., 2000. Genetic Requirements for Inheritance of RNAi in C. elegans. Science 287, 2494–2497. Katz, D.J., Edwards, T.M., Reinke, V., Kelly, W.G., 2009. A C. elegans LSD1 Demethylase Contributes to Germline Immortality by Reprogramming Epigenetic Memory. Cell 137, 308–320. Priyadarshini, M., Ni, J.Z., Vargas-Velazquez, A.M., Gu, S.G., Frøkjær-Jensen, C., 2022. Reprogramming the piRNA pathway for multiplexed and transgenerational gene silencing in C. elegans. Nat Methods 19, 187–194. Spracklin, G., Fields, B., Wan, G., Becker, D., Wallig, A., Shukla, A., Kennedy, S., 2017. The RNAi Inheritance Machinery of Caenorhabditis elegans. Genetics 206, 1403–1416. Vastenhouw, N.L., Brunschwig, K., Okihara, K.L., Müller, F., Tijsterman, M., Plasterk, R.H.A., 2006. Long-term gene silencing by RNAi. Nature 442, 882–882. Xiao, Y., Bedet, C., Robert, V.J.P., Simonet, T., Dunkelbarger, S., Rakotomalala, C., Soete, G., Korswagen, H.C., Strome, S., Palladino, F., 2011. Caenorhabditis elegans chromatin-associated proteins SET-2 and ASH-2 are differentially required for histone H3 Lys 4 methylation in embryos and adult germ cells. Proceedings of the National Academy of Sciences 108, 8305–8310. Xue, B., Leibler, S., 2016. Evolutionary learning of adaptation to varying environments through a transgenerational feedback. Proceedings of the National Academy of Sciences 113, 11266–11271.