EPISYM

Nitrogen-fixing symbioses between legumes and rhizobia are extremely valuable in sustainable agriculture. They require the formation of a specific organ, the root nodule, where nitrogen fixation and nutritional exchanges between the plant and the bacteria take place. While spectacular progress has been made on early symbiotic stages (plant-rhizobium recognition, infection and initiation of nodule formation), the understanding of how later stages of nodule development are controlled is still very limited. A key process in nodule development is a developmental transition, the coordinated differentiation of plant and bacterial cells, in order to generate the appropriate microenvironment for symbiotic nitrogen fixation. This transition results from a massive reprogramming of gene expression, with thousands of genes affected in successive waves. We have discovered that epigenetic regulations, involving plant DNA (de)methylation and small interfering RNA (siRNA) populations, are essential to produce nitrogen-fixing nodules. Our working hypothesis in the EPISYM project is that these epigenetic regulations play an important role in gene expression reprogramming associated with nodule differentiation. The dynamics of the methylome and siRNA populations during nodulation will be analyzed at genome-wide level. The role of 3 genes coding for key enzymes in the control of DNA methylation and heterochromatic-siRNA production will be characterized, both in the model legume Medicago truncatula and pea, a closely related crop species, to better understand their regulation, their impact on nodule development and their target genes. Their response to environmental conditions known to impact nodule development will also be examined. In parallel, the genome-wide dynamics of histone marks will be analyzed, in connection with symbiotic gene expression, DNA methylation as well as small and long non-coding RNAs (lncRNAs). On one hand, the integration of these data will be highly valuable for the symbiosis community via a web-accessible genome browser linking expression data (mRNAs, siRNAs and lncRNAs) with epigenetic marks (DNA and histone methylation). On the other hand, we will analyse the chromatin topology of specific symbiotic genes to dissect the relationship between 3D chromatin structure and epigenetic regulation on the reprogramming of specific expression patterns in nodule differentiation. This project will thus take advantage of the strengths and complementarity of the two Partners to conduct innovative research on this emergent theme of broad interest in biology as well as on novel types of symbiotic regulators in order to provide new strategies to improve the efficiency of nitrogen-fixing symbioses.