Doctorate thesis of National Institute of Further Education in Agricultural Science

Friday, December 8, 2017

Role of chromatin regulation in the control of gene expression in response to nitrogen variations in Arabidopsis

Fanny Bellegarde
BPMP, “Integration of nutrient signaling pathways” team

Jury :
Christel CARLES, Associate Professor, Grenoble Alpes University (Rapporteur)
Martin CRESPI, Directeur de Recherche, CNRS (Rapporteur)
Mathieu INGOUFF, Associate Professor, Montpellier University (Reviewer)
Thierry LAGRANGE, Research Director, CNRS (Reviewer)
Christian MEYER, Research Director, INRA (Reviewer)
Alain GOJON, Research Director, INRA (Thesis Director)
Antoine MARTIN, Researcher associate, CNRS (Thesis Co-Director)

Abstract :
Nitrate is an essential source of nitrogen for plants. Root nitrate transporters are subjected to transcriptional regulations that allow a fine control of nitrate uptake capacities. NRT2.1, an essential and major nitrate transporter in roots, is strongly expressed under limiting nitrate condition, and repressed under high nitrogen nutrition. This repression is correlated with an enrichment in chromatin mark H3K27me3, which seems to be dependent on the chromatin regulator HNI9. H3K27me3 is a chromatin mark repressive for gene expression, catalysed by the PRC2 complex, and involved in developmental regulation. However, the role of H3K27me3 and PRC2 in the adaptation to fluctuating nitrogen environments remains to be understood. My project was to study, in Arabidopsis, the contribution of H3K27me3 in the regulation of NRT2.1 gene in response to nitrogen provision.We demonstrate that H3K27me3 is not the major determinant of NRT2.1 repression by high nitrogen status, but that H3K27me3 directly regulates NRT2.1, in a context where NRT2.1 is strongly expressed, to temper its expression. We also show that the absence of limitation of NRT2.1 promoter hyperactivity can leads to a switch to full silencing by DNA methylation.This reveals an unexpected function of PRC2 as a safeguard for the expression of highly expressed genes. We also show that HNI9 is involved in the activation of oxidative stress responsive genes, which occurs under N-rich nutrition, and that PRC2 and NRT2.1 play independent roles in the regulation of root architecture. This work has highlighted new functions of chromatin dynamic in the regulation of genes with major significance for plant nutrition.