Journal ArticleDOI
Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
Silin Zhong,Zhangjun Fei,Zhangjun Fei,Yun-Ru Chen,Yi Zheng,Mingyun Huang,Julia Vrebalov,Ryan P. McQuinn,Nigel E. Gapper,Bao Liu,Jenny Xiang,Ying Shao,James J. Giovannoni,James J. Giovannoni +13 more
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TLDR
The 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, and Crop-improvement strategies could benefit by taking into account not only DNA sequence variation among plant lines, but also the information encoded in the epigenomes.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.read more
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Journal ArticleDOI
Dynamics and function of DNA methylation in plants.
TL;DR: DNA methylation in plants mediates gene expression, transposon silencing, chromosome interactions and genome stability, and the regulation of DNA methylation is important for plant development and for plant responses to biotic and abiotic stresses.
Journal ArticleDOI
Learning the Languages of the Chloroplast: Retrograde Signaling and Beyond
TL;DR: New findings on the processes by which organelle communication is initiated, transmitted, and perceived are discussed, not only to regulate chloroplastic processes but also to intersect with cellular signaling and alter physiological responses.
Journal ArticleDOI
Role of plant hormones and their interplay in development and ripening of fleshy fruits
TL;DR: The new knowledge on their relative roles during tomato fruit development is evaluated with a view to understand their mechanism of action in fleshy fruits and it is envisaged that such detailed knowledge will help design new strategies for effective manipulation of fruit ripening.
Journal ArticleDOI
Widespread natural variation of DNA methylation within angiosperms.
Chad E. Niederhuth,Adam J. Bewick,Lexiang Ji,Magdy S. Alabady,Kyung Do Kim,Qing Li,Nicholas A. Rohr,Aditi Rambani,John M. Burke,Joshua A. Udall,Chiedozie Egesi,Jeremy Schmutz,Jane Grimwood,Scott A. Jackson,Nathan M. Springer,Robert J. Schmitz +15 more
TL;DR: The extent of variation in DNA methylation in angiosperms is revealed and patterns are shown to be broadly a reflection of the evolutionary and life histories of plant species.
Journal ArticleDOI
Carotenoid Metabolism in Plants: The Role of Plastids.
TL;DR: This review provides a comprehensive overview of the impact of various types of plastids on carotenoid biosynthesis and accumulation, and discusses recent advances in the understanding of the regulatory control ofCarotenogenesis and metabolic engineering ofcarotenoids in light ofplastid types in plants.
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