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.

Acknowledgements

This work received financial support from the National Key R&D Program of China (Grants 2022YFD2100100 and 2021YFA1300404 to Z.L.). This study was also supported by the Guangdong S&T Program (Grant 2024B1111130001 to Z.L.) and the Shenzhen Science and Technology Program (Grants JCYJ20241202125311016 and KQTD20240729102038044 to Z.L.). The authors would like to thank Christel Renaud for her assistance with the metabolic activity analysis.

Author contributions

P.G. and Z.L. conceived and designed the research, interpreted the data, and wrote the manuscript. Y.M. and H.H. performed the bioinformatic analyses. J.K., V.G., Q.N., G.H., L.S., and S.W. prepared the experimental samples and conducted the experiments. J.K. and Q.N. carried out the sequencing work. All authors reviewed and approved the final manuscript.

Data availability

The raw sequencing data generated during this study are publicly available in the Gene Expression Omnibus (GEO) database under accession numbers GSE279794 and GSE279795 (https://www.ncbi.nlm.nih.gov/geo/). The DNase-seq data reanalyzed for this study can be found in the Sequence Read Archive (SRA) under accession number SRR5405286.

Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Supplementary data

Supplementary data is available at Horticulture Research online.

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