Global DNA-methylation is affected in G- cells. Global methylation level analysis in G− and G+ condition. (A) Bart chart representing the methylation level of individual sample (y-axis, 1 = 100%) in the three-cytosine sequence context (x-axis). (B, C) Cytosine methylation profiles within and 2 kb up- and downstream of (B) genes coding sequence and (C) of TE. (D) Differentially Methylated Cytosines (DMCs) and Differentially Methylated Regions (DMRs) and their contexts in G− condition compared to G+. Grey bar chart represents the total number of DMC/DMRs identified. Methylation changes are represented in black when methylation increases in G− compared to G+ cells (Hyperme) and in light grey when methylation decreases in G− compared to G+ cells (Hypome). Number of DMCs and DMRs are indicated on the top/bottom of each barchart. (E) Localization of identified DMRs in specific genomic features. Black and white pie charts represent the proportion of hyper-(black) and hypo-(white) methylated of identified DMRs (number underneath) in each sequence context. TE: extragenic transposable elements; TE-intron: intronic transposable elements; TE-promoter; transposable element found within promoter sequence.
Plants face constant challenges from fluctuating nutrient availability, which disrupts their growth and survival. Sugar starvation, for instance, triggers metabolic and transcriptional changes, but the role of epigenetic regulation in this process remains poorly understood. Epigenetic mechanisms, such as DNA methylation, are known to influence gene activity without altering the DNA sequence, yet their connection to metabolic stress is unclear. Previous studies in animals and yeast have linked starvation to epigenetic modifications, but evidence in plants is limited. Understanding how plants epigenetically adapt to carbon scarcity could unlock new ways to enhance their stress resilience. Based on these challenges, researchers investigated the interplay between sugar depletion, DNA methylation, and gene expression in grapevine cells.
on January 1, 2025, in , a study by scientists from the University of Bordeaux and INRAE, including Margot M.J. Berger, Virginie Garcia, Nathalie Lacrampe, and others,explores how grapevine cells respond to sugar starvation. Using Cabernet Sauvignon cell cultures, the team analyzed metabolic, transcriptional, and epigenetic changes under glucose-rich and glucose-poor conditions. The research reveals that carbon deficiency triggers widespread DNA methylation changes, particularly at transposable elements, alongside shifts in gene expression linked to stress survival. These findings underscore the importance of epigenetic regulation in plant adaptation to nutrient scarcity.
The study found that grapevine cells deprived of glucose halted growth within 48 hours and underwent dramatic metabolic reprogramming. Key pathways for biomass production, like cell wall synthesis, were downregulated, while autophagy and photosynthesis genes were activated. Notably, sugar-starved cells showed higher global DNA methylation levels, especially in transposable elements, suggesting a mechanism to stabilize the genome under stress.
Using multi-omics approaches, the team identified 5,607 differentially expressed genes and 848 differentially methylated regions (DMRs). Hyper-methylation in CHH contexts was prominent, linked to reduced cell division and altered small RNA pathways. Intriguingly, some genes involved in carbon metabolism and stress responses exhibited methylation changes in their promoters, correlating with expression shifts. For example, a malate dehydrogenase gene was repressed alongside hyper-methylation of its promoter.
The study also revealed disruptions in one-carbon metabolism, which supplies methyl groups for DNA methylation. Flux analyses showed slowed production of S-adenosylmethionine (SAM), a key methyl donor, hinting at resource reallocation during starvation. These insights highlight how epigenetic and metabolic networks jointly orchestrate plant stress responses.
Dr. Philippe Gallusci, the study’s corresponding author, emphasized: "Our work bridges the gap between metabolism and epigenetics in plants. By showing how DNA methylation dynamically responds to carbon scarcity, we uncover a layer of regulation critical for stress adaptation. This could pave the way for breeding crops with enhanced resilience by targeting epigenetic pathways."
The research opens avenues for improving crop tolerance to abiotic stresses, such as drought or poor soil, by manipulating epigenetic markers. Farmers could potentially use metabolic priming or epigenetic editing to enhance plant survival in low-nutrient conditions. Additionally, the findings may inform viticulture practices, helping grapevines withstand climate-induced sugar shortages during ripening. Future studies could explore whether similar mechanisms operate in other crops or under field conditions. By elucidating the epigenetic basis of stress responses, this work contributes to sustainable agriculture strategies aimed at securing food production in a changing climate.
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Funding information
Margot Berger was in receipt of a grant financed by CNIV (Comité National des Interprofessions du Vin) and by the Région Nouvelle Aquitaine (EPISTORE). Bernadette Rubio was in receipt of the PNDV (Plan National du dépérissement de la Vigne) funding EPIDEP. The work was supported by PNDV, Region Nouvelle Aquitaine and Bordeaux University.
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is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.
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