Molecular Plant Breeding 2025, Vol.16, No.5, 261-267 http://genbreedpublisher.com/index.php/mpb 263 crucial in the light-induced accumulation of lycopene, and this process does not rely on the production of ethylene. Environmental stress can alter DNA methylation levels by up-regulating epigenetic genes such as histone deacetylase (HDA3), and affect fruit development, ripening and lycopene content (Nazari et al., 2025). Figure 1 The regulation network of DNA methylation, RNA methylation, histone modification and non-coding RNA in tomato fruit ripening (Adopted from Ming et al., 2023) Image caption: SlALKBH2 regulates the stability of SlDML2 RNAby RNAm6A demethylation, enhancing its stability. Conversely, SlDML2 promotes the expression of SlALKBH2 through DNA demethylation, ultimately affecting fruit ripening. The histone demethylase SlJMJ6 eliminates H3K27me marks fromSlDML2, RIN and ripening-associated genes, consequently promoting fruit ripening. On the other hand, histone demethylase SlJMJ7 erases H3K4me modifications from these genes, thus contributing to the inhibition of fruit ripening. Tomato methyltransferase SlMET1, Histone deacetylases SlHDA1, SlHDA3 and SlHDT1 may negatively regulate ripening-associated genes to control fruit ripening, while SlHDT3 exhibits opposing regulatory effects. PRC1 protein SlLHP1b could bind H3K27me mark in regions of ripening-associated chromatin, targeting ripening-related genes, repressing fruit ripening. Meanwhile, SlLHP1b interacted with PRC2 protein SlMSI1, negatively regulating tomato fruit ripening. The microRNA gene SlMIR164Awas involved in negative regulation of tomato fruit ripening (Adopted from Ming et al., 2023) 4.2 Hormonal regulation (ethylene, ABA) mediated by epigenetic mechanisms Ethylene is the main hormone regulating the ripening of tomato fruits and the accumulation of lycopene. Epigenetic mechanisms are closely related to the ethylene signaling pathway. Studies have found that the silencing of histone deacetylases (such as SlHDA1, SlHDA3, etc.) will accelerate fruit ripening, while their upregulation will delay ripening and indirectly affect the accumulation of lycopene (Nazari et al., 2025). Ming et al. (2023) demonstrated in their research that hormones such as abscisic acid (ABA) may also influence the expression of related genes by regulating epigenetic modifications, but the specific mechanisms still require further study. 4.3 Crosstalk between metabolic pathways and epigenetic regulation The biosynthesis of lycopene involves multiple metabolic pathways, and the expression of key enzyme genes in these pathways is regulated by epigenetic modifications. The histone variant Sl_H2A.Z regulates the expression of genes related to carotenoid biosynthesis (such as SlPSY1, SlPDS, etc.) and affects lycopene accumulation (Ming et al., 2023). Non-coding RNAs are involved in the regulation of fruit ripening and pigment accumulation by targeting key genes in metabolic pathways (Chen et al., 2018; Ming et al., 2023). The interaction between epigenetic mechanisms and metabolic networks together constitutes a complex system for regulating lycopene accumulation.
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