Response of grape cells in culture to carbon shortage - From metabolic response to epigenetic regulations

Epigenetics corresponds to the complement of genetic information carried in chromatin beyond the DNA sequence. It includes the post translational modification of histone and DNA methylation, both involved in the control of gene expression and transposon mobility. Epigenetic marks deposition and removal depends on metabolic precursor and co-factor availability. Epigenetic regulations are therefore depending on the cell metabolic balance, itself regulated by various cellular processes (cell division, response to environmental changes …). For the first time in grapevine, this work aimed to evaluate the consequences of carbon deficiency on cell phenotypes, metabolism, gene expression and methylome. Cabernet Sauvignon cells derived from fruit tissues were cultivated in the presence or absence of glucose. Results show that two days after glucose deprivation, the cell metabolism is dramatically slow down, and cell proliferation is dramatically reduced. The severe limitation of sugar availability leads to a profound remodelling of gene expression profiles as illustrated by the identification of 6000 DEGs. Results indicate that genes involved in photosynthetic processes and metabolic regulations are upregulated in the absence of sugar whereas those involved in the regulation of chromatin dynamic, or the synthesis of amino acids are down regulated. Methylome analysis indicate that whereas DNA methylation increase upon carbon limitation, various genes present differential methylation that are for some of them related to change in expression profiles. Links between limitation of carbon availability, cell metabolism and gene expression and epigenetic regulations are discussed.