The grape berry methylome reveals tissue-specific features associated with metabolism in ripening

Abstract DNA methylation is a critical epigenetic regulator in plant development, yet its role in grape berry ripening remains poorly understood. Here, we profiled the genome-wide DNA methylation landscapes of two cultivars, ‘Wink’ and ‘Cabernet Sauvignon’, across developmental stages and tissues (skin and pulp tissues), revealing widespread DNA hypermethylation during ripening. We observed a progressive increase in global DNA methylation, particularly in the CHH context, across transposable elements, gene bodies, and adjacent regions during ripening. This hypermethylation was conserved across both varieties and was pronounced in both skin and pulp tissues. Differentially methylated regions (DMRs) revealed tissue-specific methylation patterns, with skin and pulp exhibiting distinct hypermethylation dynamics. Further analysis demonstrated that these tissue-specific hypermethylation dynamics are partially attributable to pre-existing methylation differences between skin and pulp at earlier developmental stages. Functional analysis demonstrated that DNA methylation inhibitors (zebularine and RG108) delayed berry ripening in vitro, underscoring the critical role of methylation in this process. Furthermore, RNA-seq analysis identified tissue-specific gene expression changes associated with differential methylation, particularly in metabolic pathways such as anthocyanin biosynthesis, fructose metabolism, and glycolysis. Notably, tissue-specific hypermethylation of genes involved in anthocyanin metabolism correlated with their expression patterns, suggesting a regulatory role for DNA methylation in metabolite accumulation during ripening. Collectively, these findings underscore DNA methylation as a critical regulatory layer that orchestrates tissue-specific gene expression with metabolic shifts during grape maturation, thereby advancing our understanding of epigenetic control in fruit development.