Epigenetic Natural varIation in Arabidopsis – ENIgmA

Nous utilisons des approches classiques de recherche de QTL chez l’espèce modèle Arabidopsis thaliana. Certains de ceux que nous avons identifiés sont liés à des marques épigénétiques. Nous caractérisons les mécanismes moléculaires mis en jeu ainsi que la façon dont ces marques sont transmises de manière stable au cours des générations.

Nous avons déjà montré qu’une forme d’incompatibilité épigénétique entre deux accessions de la plante modèle Arabidopsis est liée à des marques épigénétiques différentes et est basée sur deux régions chromosomiques différentes.

Nous cherchons maintenant à savoir comment certaines marques épigénétiques sont déposées et ce qui conditionne leur maintien au cours des générations.

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Epigenetic is defined as the study of heritable modifications in gene expression without changes in DNA sequence. Behind this very straightforward definition, the complex mechanisms underlying epigenetic modifications and chromatin dynamic are now very widely studied, in particular in plant models such as Arabidopsis. Recent high-throughput analyses revealed the epigenetic landscapes of Arabidopsis like variations in DNA methylation, histone modifications and small RNAs abundance, as well as epigenetic polymorphisms in transcribed regions of different accessions. Studies of plant natural variation have been focused mainly on sequence variation, and little is known about the role of epigenetic machinery in these processes. We now clearly need to isolate and study more epialleles to understand the significance of inherited epigenetic alterations in natural populations.
In the Institut Jean Pierre Bourgin, several groups are interested in the analysis of Arabidopsis natural variation as a source of biodiversity. Many different quantitative trait loci (QTL) responsible for these variations were determined and the genes underlying these QTLs revealed. Interestingly, genes for which the polymorphism observed at the nucleotide level in the parental accessions cannot explain the phenotype of certain recombinant inbred lines (RILs), were also identified. The objective of this project is to characterize natural epivariants with phenotypic consequences and investigate the mechanisms underlying them.
The first part of the project will focus on a new epiQTL, SG1. We believe that the SG1 protein is involved directly or indirectly in the epigenetic control of certain loci, including itself. Preliminary results have shown that SG1 is more methylated in certain accessions. The analyse of the profiles of DNA methylation and histone modifications will be further determined. We will identify the partners of the SG1 protein, its cellular localisation and targets. Finally, we will characterise the epimutants generated in a sg1 context since sg1 T-DNA mutants isolated in Col present stochastic phenotypes appearing after several generations and being reminiscent of epimutations.
The second part of the project will focus on an incompatibility resulting from the Sha x Col cross. Preliminary analysis revealed a polymorphism of methylation between the two accessions at a locus on chromosome 5 (AtFOLT1 gene; transporter of folate). This could be explained by the presence of a second locus at chromosome 4 (AtFOLT2) suspected to be the origin of the methylation at chromosome 5 in Sha. First, we will reveal, the specific molecular structures (like tandem repeats) existing at incompatible loci in different accessions. The epigenetic marks of these regions will be determined. We will test whether incompatible loci are sufficient to trigger de novo DNA methylation and we will determine the molecular pathways that control these epigenetic variations. Since the first submission of this proposal in 2010, we have detected small RNAs targeting AtFOLT1 that will be further characterized in other accessions.
Finally, since recent data point toward the fact that natural genetic variations modulate the biogenesis of small RNAs in Arabidopsis. We identified expression QTLs (eQTL) corresponding to genes involved in the biogenesis of small RNAs in two mapping populations. This exciting project will be further developed.
We are in a very favorable position to characterize these new natural epivariants with the combination of our expertise on Arabidopsis epigenetics and the unique discovery of natural epivariants. This project is opening the way to a new challenging topic emerging in the natural variation field that will undoubtedly lead to the discovery of more examples of epigenetic mechanisms imparting information that regulates gene expression across generations.