Research axes
Axis 1. Epigenetics, transcription and transposable elements (PI: Guillaume Moissiard and Nathalie Picault).
Our team studies epigenetic pathways and chromatin factors regulating gene expression and repressing transposable elements (TEs). We are also characterizing the function of TE genes that have been exapted – also known as coopted or domesticated – by the plants. These genes, called exapted TE (ETE) genes can be of different origins, forming distinct gene families such as the Plant Mobile Domain, the MUSTANG or the SLEEPER families. Finally, we are studying the impact of TEs on transcriptomic diversity in plants subjected to abiotic stresses such as heat to understand how TEs can contribute to plant adaptation in response to environmental stresses.
Our research is mostly done in Arabidopsis and tomato, two plant species displaying very different genome organizations. We combine Illumina short-read and Oxford Nanopore technologies (ONT) long-read sequencing to study differential gene expression, full length RNA diversity, structural variations and epigenetic modifications. We use biochemical approaches to study chromatin/protein interaction (ChIP-seq) and protein interaction (IP-MS, CLNIP-MS, Co-IP, FPLC…).
Axis 2: Gene dose and dosage control (PI: Frédéric Pontvianne).
The aim of our group is to understand the mechanisms that regulate gene expression before transcription begins. Transcription of a gene, or any other transcribed element is only possible when the locus is accessible. In other words, it must be located in a region of the nucleus open to transcription factors and have an epigenetic signature compatible with transcriptional activity. The three-dimensional organization of the genome in the nucleus plays a key role in this regulation, as well as chromatin modifications such as DNA methylation and post-translational histone modifications.
In our team, we are studying this regulation at the allelic level using approaches: (i) either genomics (CITRUS project) when nucleotide variation is present, using citrus fruit as a model, (ii) or microscopy (POSITIONING project) when the alleles have the same nucleotide sequence, using Arabidopsis thaliana as a model.
Keywords : Epigenetics, transcription, transposable elements, exaptation, live-cell Imaging
Funding
- ANR PolyPMD (ANR-23-CE20-0012; 01/2024-06/2028): Antagonism between Plant Mobile Domain-containing proteins and Polycomb-mediated gene silencing. Partners: Olivier Mathieu (coordinator, iGred, Clermont-Ferrand) and Guillaume Moissiard.
- New Frontiers TULIP LabEx (06/2022-12/2024): Impact of transposons on plant adaptation and development by alternative splicing. Coordinators: Nathalie Picault and Guillaume Moissiard.
- ANR DYSCORD (ANR-23-CE20-0036-03; 2024-2028): Dynamics of chromosome organization during reproductive development. Partners: Mathieu Ingouff (coordinator, IRD, Montpellier), Mathilde Grelon (IJPB, INRAe Versailles) et Frédéric Pontvianne.
- ANR Mobil-DNA (ANR-24-CE20-6240-03; 2025-2029): T-DNA fate, regulation and impact during Agrobacterium-Arabidopsis interaction. Partners: Denis Faure (coordinator, I2BC, Saclay), Angélique Déléris (I2BC, Saclay) et Frédéric Pontvianne.
Team members
Publications
- Research and reviews articles
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- Communications
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- PhD thesis and HDR
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