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. Finally, we are studying the impact of TEs on (epi)transcriptomic diversity in plants subjected to abiotic stresses such as heat to understand how TEs contribute to plant adaptation to environmental constraints.
Background
TEs are highly repeated, self-replicating mobile elements, capable of propagating in the genomes by a mechanism called transposition. TEs are virtually present in all plant genomes, ranging from ~20% in A. thaliana to 62% in tomato and 85% in maize. Upon transposition, TEs can differently impact the host genome. Firstly, and most of the time, TE neo-insertions are neutral, for instance, when they insert into non-regulatory intergenic regions. Secondly, they can be mutagenic, by disrupting the sequence of protein-coding genes, or provoking chromosomal rearrangement. That is why TEs are tightly regulated by the cell by several mechanisms including epigenetic pathways. Finally, a TE neo-insertion can occasionally provide positive advantage for the host, hence entering natural selection processes. Through their great diversity, TEs can thus contribute to the evolution of host species by supplying genetic innovation. In conclusion, the host-TE interaction relies on a tight and complex relationship, from conflict (or arms race), cooperation (or equilibrium) to exaptation (or co-option).
TE exaptation -also known as co-option or domestication - occurs at the macroevolution scale, and can involve TE-derived coding or non-coding sequences. As TEs encode diverse protein domains with specialized molecular functions, such as for instance transposases, integrases or reverse transcriptases, as well as structural and envelope proteins; they can be a great source of genetic innovation for the host genome.
In plants, good examples of exapted TE (ETE) gene families are the FAR-RED IMPAIRED RESPONSE 1 / FAR-RED ELONGATED HYPOCOTYLS3 (FAR1/FHY3), the MUSTANG (MUG), the SLEEPER, the PIF/Harbinger-Related ETE… Besides, Plant Mobile Domain (PMD) proteins are good examples of plant genes that are widely associated to TEs.
Research axes
Our research is organized in two main axes that study TEs as a source of genetic innovation.
- Axis 1. We functionally characterize the mode of action of exapted TE (ETE) genes and TE-associated proteins during plant development and in response to environmental constraints. We have also developed bioinformatic approach to identify putative ETE genes in plant genomes.
- Axis 2. We study the impact of intragenic TEs – that are located within host genes, on (epi)transcriptional diversity in plants subjected to abiotic stresses.
Our research is mostly done in Arabidopsis thaliana and Solanum lycopersicum (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 and epitranscriptomics, structural variations and epigenetic modifications. We use biochemical approaches to study chromatin/protein interaction (ChIP-seq) and protein interaction (IP-MS, Co-IP, FPLC…).
If you are interested in our research, do not hesitate to reach out!
Keywords : Epigenetics, transcription, transposable elements, exaptation, stress, plant adaptation
Funding
- ANR SollycPMD (ANR-26-CE20; 01/2027-12/2030): Functional characterization of Plant Mobile Domain proteins in Solanum lycopersicum. Partners: Guillaume Moissiard (coordinator), Julien Pirrello (GBF, Toulouse) and Christian Chevalier (BFP, Bordeaux).
- 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.
Team members
Alumni
Publications
- Research and reviews articles
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- Communications
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- PhD thesis and HDR
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