DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening

Gallusci, Philippe; Hodgman, Charlie; Teyssier, Emeline; Seymour, Graham B.

doi:10.3389/fpls.2016.00807

Cited by 119 publications

(90 citation statements)

References 108 publications

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“…Several of these were found to be orthologous to genes that are known to be important regulators of flower and fruit development in other species. This suggests that apple fruit development is regulated by epigenetic processes, which is consistent with data obtained in tomato, demonstrating that DNA methylation is important for fruit ripening [56][57][58] .…”

Section: Discussionsupporting

confidence: 89%

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

et al. 2017

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Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

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Section: Discussionsupporting

confidence: 89%

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

et al. 2017

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“…DNA methylation has been shown to be involved in fruit ripening (Gallusci et al, 2016). Genomic DNA cytosine methylation from tomato pericarps was decreased prior to ripening initiation (Cao et al, 2014).…”

Section: Analysis Of Genes Involved In Cell Wall Degradationmentioning

confidence: 99%

Transcriptomic Analysis on the Regulation of Tomato Ripening by the Ethylene Inhibitor 1-methylcyclopropene

Bobokalonov¹,

Liu²,

Shahrin³

et al. 2018

JPS

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Tomato is a climacteric fruit whose ripening is regulated by the plant hormone ethylene. 1-methylcyclopropene (1-MCP) is a competitive ethylene inhibitor that can delay the fruit ripening process. To understand the molecular mechanism of how 1-MCP inhibits tomato fruit ripening, transcriptomics (RNA-Seq) was used to identify genes that were differentially expressed in 1-MCP-treated (Day 1) tomato fruits. Of the 35340 genes in the tomato genome, about 50% were expressed with 1-MCP treatment. There were 5683 genes identified as significantly differentially expressed. Quantitative reverse transcription PCR (qRT-PCR) assays were used to validate the RNA-Seq data. Our results showed that 1-MCP treatment resulted in the down-regulation of fruit ripening-related genes, including genes involved in ethylene synthesis, signal transduction and carotenoid biosynthesis. Our results provide insight at the whole genome level regarding gene regulation by 1-MCP during fruit ripening. Understanding the molecular basis of 1-MCP inhibition on tomato ripening may help farmers and food processors to better use 1-MCP in agriculture and food industry.

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“…The epigenetic changes may lead to chromatin modifications which may cause a stable alteration in transcriptional activity even after withdrawal of the triggering stress/signal [18]. Epigenetic regulation of gene expression is mediated by a complex interplay among different molecular factors which include DNA methylation/demethylation, the enzymes involved in post-translational modifications of histone proteins, chromatin remodelers and small RNAs [19][20][21]. Methylated cytosine has been observed to be involved in silencing of TEs, regulation of important developmental processes, genome imprinting and stress responses in both plants and animals [22][23][24].…”

Section: Introductionmentioning

confidence: 99%

Epigenomics of Plant’s Responses to Environmental Stress

Kumar¹

2017

Preprint

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Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of small non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant's responses to environmental stresses for climate resilient agriculture.

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DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening

Cited by 119 publications

References 108 publications

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Transcriptomic Analysis on the Regulation of Tomato Ripening by the Ethylene Inhibitor 1-methylcyclopropene

Epigenomics of Plant’s Responses to Environmental Stress

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