Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

Abstract

Ripening of tomato fruits is triggered by the plant hormone ethylene, but its effect is restricted by an unknown developmental cue to mature fruits containing viable seeds. To determine whether this cue involves epigenetic remodeling, we expose tomatoes to the methyltransferase inhibitor 5-azacytidine and find that they ripen prematurely. We performed whole-genome bisulfite sequencing on fruit in four stages of development, from immature to ripe. We identified 52,095 differentially methylated regions (representing 1% of the genome) in the 90% of the genome covered by our analysis. Furthermore, binding sites for RIN, one of the main ripening transcription factors, are frequently localized in the demethylated regions of the promoters of numerous ripening genes, and binding occurs in concert with demethylation. Our data show that the epigenome is not static during development and may have been selected to ensure the fidelity of developmental processes such as ripening. Crop-improvement strategies could benefit by taking into account not only DNA sequence variation among plant lines, but also the information encoded in the epigenome.

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

“…During tomato fruit ripening, DNA demethylation occurs in numerous genomic regions (27). In tomato, there are four annotated 5-mC DNA glycosylase/DNA demethylase genes; one of them, SlDML2, is highly induced during fruit ripening (29,30).…”

“…These regulators function upstream of both ethylenedependent and -independent ripening pathways by directly and indirectly regulating the expression of many ripening-related genes (24)(25)(26). Evidence has recently emerged that, in addition to ethylene and the TFs, DNA methylation is another key regulator of fruit ripening (27). Furthermore, a recent study revealed that DNA methylation is associated with chilling-induced flavor loss in tomato fruits (28).…”

“…Furthermore, a recent study revealed that DNA methylation is associated with chilling-induced flavor loss in tomato fruits (28). Tomato fruits undergo a dramatic loss in DNA methylation during ripening (27). The application of a DNA methylation inhibitor facilitated ripening, and RNAi-mediated down-regulation of putative DNA demethylases inhibited fruit ripening in tomato, suggesting that active DNA demethylation plays an important role in regulating fruit ripening (27,29).…”

“…Tomato fruits undergo a dramatic loss in DNA methylation during ripening (27). The application of a DNA methylation inhibitor facilitated ripening, and RNAi-mediated down-regulation of putative DNA demethylases inhibited fruit ripening in tomato, suggesting that active DNA demethylation plays an important role in regulating fruit ripening (27,29). It remains unclear, however, how active DNA demethylation contributes to ripening and ripening-associated changes in DNA methylation patterns.…”

Mobile small RNAs and their role in regulating cytosine methylation of DNA

“…3 Gene silencing is involved in several biological processes of plants, including defending the genome from transposable elements (TEs), development, imprinting, environmental responses and stress memory. [3][4][5][6][7][8][9][10][11] Cytosine residues of DNA can be modified by the addition of a methyl group. This is associated with transcriptional gene silencing and formation of repressive chromatin, influencing potentially both structure and function of target loci.…”