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Département Biologie des Génomes

par Clubs génome, EQYY - publié le , mis à jour le


  • Vendredi 25 janvier 11:00-12:00 - Nathalie Beaujean - Stem Cell & Brain Institute – Lyon

    Epigenetic reprogramming of rabbit stem cells

    Résumé : Abstract
    Pluripotency is the term used to describe the ability of a stem cell to give rise to all cell types in mature organisms. Two main types of pluripotent stem cells (PSCs) have been described : naïve and primed. The naïve pluripotent state is characteristic of mouse embryonic stem cells (mESCs) and developmentally corresponds to the early epiblast component of the blastocyst stage (just before implantation). Under appropriate conditions, mESCs exhibit unlimited self-renewal capacity while retaining the attributes of preimplantation epiblast identity and potency – especially the ability to generate chimeras.
    On the other hand, in non-rodent species, including humans, it is challenging to capture this original “embryonic” state of pluripotency in PSCs that are mostly in the primed state. In particular, the scarcity of primate embryos makes it difficult to address this issue. As a surrogate model, the rabbit is perfectly suited to explore the nature and mechanisms of acquisition and maintenance of pluripotency in the epiblast cells and ESCs. We therefore explore naïve pluripotency in the rabbit.
    We characterised the transcriptome of the rabbit epiblast throughout pre-implantation development using single-cell analysis. We observed a transcriptomic continuum of pluripotency in vivo specific to the rabbit, although we observed many similarities to the mouse. We also identified new genes and rabbit-specific markers of naïve pluripotency that could be used for reprogramming conventional rabbit PSCs to naïve-state pluripotency ; in particular genes related to the epigenome reprogramming occurring during embryonic development such as the histone acetyltransferase Kat8. We are now implementing new strategies using the identified markers to reprogram rabbit PSCs towards the naïve state. These results will allow us to judge the state of pluripotency of rabbit PSCs we will derive in vitro, as compared to the embryo.
    Contact : Daan Noordermeer <daan.noordermeer>

    Lieu : Bibliothèque- bâtiment 34 - Campus CNRS de Gif-sur-Yvette

  • Vendredi 1er février 11:00-12:00 - Eugene Gladyshev - Institut Pasteur

    Recombination-independent recognition of DNA homology for meiotic silencing in Neurospora crassa

    Résumé : Homologous chromosome pairing represents a critical aspect of meiosis in nearly all sexually reproducing organisms. While in some species this process depends on the formation of double-strand DNA breaks, in the others it can proceed (partially or completely) in the apparent absence of DNA breakage and recombination. The nature of a mechanism that can identify intact homologous chromosomes represents a fundamental question in molecular biology. Using “meiotic silencing by unpaired DNA” (MSUD) in Neurospora crassa as a model system, we demonstrate the existence of a cardinally new solution to the problem of DNA homology recognition during meiosis. Here we take advantage of the unique ability of MSUD to detect and silence (by RNA interference) any relatively short fragment of genomic DNA present on only one of the two homologous chromosomes. Specifically, we show that MSUD does not require the function of eukaryotic RecA proteins (Rad51/Dmc1) and the type II topoisomerase-like protein Spo11. We further show that MSUD can recognize patterns of weak interspersed homology in which triplet units of sequence identity are arrayed with a periodicity of 11 base-pairs. In doing so, MSUD shares its basis for homology recognition with “repeat-induced point mutation” (RIP), a prototypical genome-defense phenomenon that is activated in premeiotic nuclei of N. crassa and many other filamentous fungi. Taken together, these results reveal the role of a recombination-independent homology-directed process in guiding the expression of small interfering RNAs and, more broadly, suggest that meiotic chromosomes can be evaluated for homology at the base-pair resolution by a mechanism that operates on intact DNA double helices.
    Contact : Fabienne Malagnac <fabienne.malagnac>

    Lieu : Salle Kalogeropoulos - Bât. 400 - Campus d’Orsay

  • Vendredi 15 février 11:00-12:00 - Martial Marbouty - Institut Pasteur

    Contact genomic : a new tool to study microbial communities and unveil mobile elements - bacteria relationships in mammalian gut microbiota

    Résumé : Metagenome sequence analysis relies principally on compositional approaches, which hypothesise that sequences sharing similar characteristics (GC%, codon bias, coverage-covariation... etc.) should share the same cellular compartment. Although these approaches have generated important results, they remain somehow limited and do not allow the full characterization and understanding of the genetic composition of a complex microbial population. Contact genomics, which aimed at exploiting the 3D physical signature of genomes to solve their sequence, has the potential to alleviate or improve some of these caveats. To explore the genomic content of bacterial populations at a new level of resolution, we have recently developed meta3C (Marbouty et al. 2014), a derivative protocol of the chromosome conformation capture (3C ; Dekker et al. 2002) assay that aims at deciphering the average 3D organization of a genome. Using controlled mixes of bacterial or yeast species, we showed that the frequent collisions experienced by DNA molecules sharing similar cellular compartments can be measured through meta3C and conveniently used to assemble larger scaffolds of the genomes present in a metapopulation.
    Here I will present data obtained from different samples of mammalian gut microbiota (Marbouty et al. 2017). Meta3C allows unveiling hundreds of genomic compartments, hence species. Moreover, Meta3C allows to link mobile genetic element sequences to their bacterial host and provide a convenient way to study interactions between genomic entities in a complex population. I will discuss the different ways to explore this network and the results in light of the promising potential of the approach for future applications.
    Contact : Mireille Bétermier <mireille.betermier>

    Lieu : Salle des séminaires- bâtiment 26 - Campus CNRS de Gif-sur-Yvette

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