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

TitleSingle-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening.
Publication TypeJournal Article
Year of Publication2013
AuthorsZhong S, Fei Z, Chen Y-R, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, Liu B, Xiang JZ, Shao Y, Giovannoni JJ
JournalNat Biotechnol
Volume31
Issue2
Pagination154-9
Date Published2013 Feb
ISSN1546-1696
KeywordsAzacitidine, Base Sequence, Binding Sites, Chromosome Mapping, DNA Methylation, Epigenesis, Genetic, Ethylenes, Fruit, Gene Expression Regulation, Plant, Lycopersicon esculentum, Methyltransferases
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.

DOI10.1038/nbt.2462
Alternate JournalNat. Biotechnol.
PubMed ID23354102

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