表观遗传调控番茄果实发育及成熟的进展

doi:10.13560/j.cnki.biotech.bull.1985.2025-1303

摘要/Abstract

摘要：

肉质果实是被子植物特有的结构，对种子的保护和传播起着重要作用，可显著提高种子的传播效率。番茄作为研究园艺作物的模式植物，其果实发育与成熟是一个受遗传、激素、环境因子多层次调控的高度复杂且精细的生物学过程，直接影响果实大小、色泽转变、可溶性糖积累和果实软化等。表观遗传修饰通过调节染色质结构和基因可及性，在园艺作物果实发育和成熟相关基因的动态表达调控中发挥核心作用。本文综述了近年来表观遗传修饰在番茄果实发育和成熟中的分子调控研究进展，系统梳理DNA/RNA甲基化、组蛋白修饰、非编码RNA修饰在番茄果实发育和成熟转录调控网络中的重要功能以及协同作用机制。同时，对目前研究的局限性和未来发展方向进行了讨论，期望利用多组学、单细胞测序和人工智能等技术手段，揭示环境因子整合与表观遗传调控的分子机制，为果实品质改良和分子育种提供理论基础和应用前景。

关键词: 表观遗传, 番茄, 果实发育, 果实成熟, 转录调控, 分子机制

Abstract:

Fleshy fruits are an angiosperm-specific hallmark and are essential for seed protection and dispersal, thereby markedly enhancing seed dispersal efficiency. As a premier model of horticultural crops, tomato (Solanum lycopersicum) development and ripening are highly complicated and precisely coordinated biological processes governed by genetic programs, phytohormonal signaling and environmental factors. These regulatory networks directly affect fruit size, color changes, soluble sugar accumulation, and fruit softening. Epigenetic modifications fine-tune dynamic gene expression changes during fruit development and ripening by modulating chromatin structure and gene accessibility. In this review, we provide an overview of the significant studies on the epigenetic mechanisms of tomato fruit development and ripening. Then we systematically outline the functions of DNA and RNA methylation, histone modifications, and non-coding RNA modifications, and highlight their coordinated roles within transcriptional regulatory networks of tomato fruit development and ripening. In addition, this review discusses current limitations and explores future direction in this field. Future research should emphasize the integration of multi-omics, single-cell sequencing, and artificial intelligence technologies to uncover the molecular mechanisms of environmental factors integration and epigenetic regulation, ultimately providing a theoretical basis and application prospects for fruit quality improvement and molecular breeding.

Key words: epigenetic regulation, tomato, fruit development, fruit ripening, transcriptional regulation, molecular mechanisms

刘娜, 曾宝珍, 贾兆星, 祝英方. 表观遗传调控番茄果实发育及成熟的进展[J]. 生物技术通报, doi: 10.13560/j.cnki.biotech.bull.1985.2025-1303.

LIU Na, ZENG Bao-zhen, JIA Zhao-xing, ZHU Ying-fang. Advances in Epigenetic Regulation of Tomato Fruit Development and Ripening[J]. Biotechnology Bulletin, doi: 10.13560/j.cnki.biotech.bull.1985.2025-1303.

图/表 3

图1 番茄果实成熟过程中表观遗传修饰的动态变化↑：升高；↓：降低；：DNA甲基化；：m6A甲基化；：组蛋白甲基化；：组蛋白乙酰化

Fig. 1 Dynamic changes in epigenetic modification during fruit ripening of tomato ( Solanum lycopersicum)↑: Increase. ↓: Decrease. : DNA methylation. : m6A methylation. : Histone methylation. : Histone acetylation

图2 番茄果实发育和成熟的表观遗传调控网络番茄果实发育过程中，SlSDG2与SlCMT3a协同抑制细胞增殖，而SlMSI2介导SDG2的泛素化降解，从而调控果实生长。microRNA通过靶向生长相关基因，参与果实大小调控。果实成熟阶段，SlALKBH2通过RNA m6A去甲基化调节SlDML2转录本稳定性。反之，SlDML2又通过DNA去甲基化促进SlALKBH2的表达，形成反馈回路调控果实成熟。组蛋白去甲基化酶SlJMJ6通过去除DML2、RIN及成熟相关基因的H3K27me标记促进果实成熟。而SlJMJ7则介导这些基因H3K4me修饰的去除，进而抑制果实成熟。DNA甲基转移酶SlMET1和SlCMT4、组蛋白去乙酰化酶SlHDA1、SlHDA3和SlHDT1负调控果实成熟，而组蛋白乙酰化酶SlHAF1及组蛋白去乙酰化酶SlHDT3发挥相反作用。此外，PRC1/PRC2复合体组分通过沉积H3K27me，抑制成熟相关基因表达，延缓果实成熟。非编码RNA，包括miR164A和lncRNA1471参与番茄果实成熟的负调控

Fig. 2 Epigenetic regulatory networks of tomato fruit development and ripeningDuring fruit development, SlSDG2 coordinates with SlCMT3a to negatively regulate cell proliferation, whereas SlSDG2 is ubiquitinated for degradation mediated by SlMSI2. microRNA is involved in regulating fruit size by targeting growth-related genes. During the fruit ripening stage, SlALKBH2 regulates the stability of SlDML2 transcripts through RNA m6A demethylation. Conversely, SlDML2 promotes the expressions of SlALKBH2 via DNA demethylation, forming a feedback loop that modulates fruit ripening. The histone demethylase SlJMJ6 promotes fruit ripening by removing the repressive H3K27me marks from SlDML2, RIN and other ripening-related genes, whereas SlJMJ7 suppresses fruit ripening by erasing the activating H3K4me marks from these loci. DNA methyltransferase SlMET1 and SlCMT4, together with histone deacetylases SlHDA1, SlHDA3 and SlHDT1, negatively regulate ripening-related genes to control fruit ripening, while histone acetyltransferase SlHAF1 and histone deacetylase SlHDT3 exert opposite regulatory effects. In addition, the components of PRC1 and PRC2 complexes deposit the H3K27me marks on ripening-related genes, thereby repressing fruit ripening. Non-coding RNAs, including miR164A and lncRNA1471, are also involved in the negative regulation of tomato fruit ripening

表1 番茄果实发育和成熟中表观遗传调控的研究概况

Table 1 Overview of epigenetic regulations involved in tomato fruit development and ripening

表观遗传修饰 Epigenetic modification	表观遗传因子 Epigenetic factors	生物功能 Biological function	参考文献 Reference
DNA甲基化 DNA methylation	SlDML2	dml2突变，DNA甲基化升高，果实成熟延迟	［33-35］
	SlCMT/DRM	果实发育早期表达，随着果实成熟，表达量下降	［30］
	SlMETL	成熟果实中表达丰度最高	［30］
	SlMET1	met1突变，叶片组织的甲基化整体降低，RIN靶基因ACC2在叶片中异位表达	［31］
	SlCMT4	突变后，呈现叶小且厚、侧芽增加、花蕊异常、果实小、结实率低等生长发育缺陷	［32］
RNA甲基化 RNA methylation	SlALKBH2	敲除后，降低SlDML2表达，延迟果实成熟	［38］
组蛋白修饰 Histone modification	SlHAF1	促进果实成熟	［40］
	SlHAM1	种子和果实发育中表达	［40］
	SlHDA1	果实成熟负调控因子；还能够与SlERF.F12，TPL蛋白形成三元复合物，抑制关键成熟相关基因，延缓果实成熟	［43，48］
	SlHDA3	突变后乙烯和番茄红素合成积累，加速果实成熟	［44］
	SlHDA7	通过调控成熟相关基因表达，促进果实成熟	［46］
	SlHDT1	沉默后，果实成熟加快	［45］
	SlHDT3	沉默后，延缓果实成熟	［47］
	SlSDG33/SlSDG8	参与果实成熟	［40］
	SlEZ1/SlEZ2	SlEZ1调控果实发育，SlEZ2调控成熟	［53］
	SlSDG2	与DNA甲基转移酶SlCMT3a协同调控果实大小，又能被SlCUL4泛素化降解	［55］
	SlLHP1b	一方面与SlMSI1相互作用，调控果实成熟；另一方面与SlHDA1互作，招募转录因子SlPLT6，抑制果实成熟	［56-57］
	SlJMJ3	过表达促进果实成熟	［58］
	SlJMJ6	通过去除H3K27甲基化，并上调SlDML2表达，促进果实成熟	［59］
	SlJMJ7	果实成熟负调控因子，功能缺失后，激活成熟相关基因和DML2的表达，促进果实成熟	［60］
非编码RNA	microRNA164A	过表达延缓番茄成熟	［69］
Non-coding RNA	Sly-miR159	靶向赤霉素相关基因，影响果实形状和大小	［70］
	Sly-miR167	抑制生长素响应基因，参与腔室和胎座发育	［71］
	lncRNA1471	结合转录因子ASR，参与果实成熟	［72］

表1 番茄果实发育和成熟中表观遗传调控的研究概况

Table 1 Overview of epigenetic regulations involved in tomato fruit development and ripening

表观遗传修饰 Epigenetic modification	表观遗传因子 Epigenetic factors	生物功能 Biological function	参考文献 Reference
DNA甲基化 DNA methylation	SlDML2	dml2突变，DNA甲基化升高，果实成熟延迟	［33-35］
	SlCMT/DRM	果实发育早期表达，随着果实成熟，表达量下降	［30］
	SlMETL	成熟果实中表达丰度最高	［30］
	SlMET1	met1突变，叶片组织的甲基化整体降低，RIN靶基因ACC2在叶片中异位表达	［31］
	SlCMT4	突变后，呈现叶小且厚、侧芽增加、花蕊异常、果实小、结实率低等生长发育缺陷	［32］
RNA甲基化 RNA methylation	SlALKBH2	敲除后，降低SlDML2表达，延迟果实成熟	［38］
组蛋白修饰 Histone modification	SlHAF1	促进果实成熟	［40］
	SlHAM1	种子和果实发育中表达	［40］
	SlHDA1	果实成熟负调控因子；还能够与SlERF.F12，TPL蛋白形成三元复合物，抑制关键成熟相关基因，延缓果实成熟	［43，48］
	SlHDA3	突变后乙烯和番茄红素合成积累，加速果实成熟	［44］
	SlHDA7	通过调控成熟相关基因表达，促进果实成熟	［46］
	SlHDT1	沉默后，果实成熟加快	［45］
	SlHDT3	沉默后，延缓果实成熟	［47］
	SlSDG33/SlSDG8	参与果实成熟	［40］
	SlEZ1/SlEZ2	SlEZ1调控果实发育，SlEZ2调控成熟	［53］
	SlSDG2	与DNA甲基转移酶SlCMT3a协同调控果实大小，又能被SlCUL4泛素化降解	［55］
	SlLHP1b	一方面与SlMSI1相互作用，调控果实成熟；另一方面与SlHDA1互作，招募转录因子SlPLT6，抑制果实成熟	［56-57］
	SlJMJ3	过表达促进果实成熟	［58］
	SlJMJ6	通过去除H3K27甲基化，并上调SlDML2表达，促进果实成熟	［59］
	SlJMJ7	果实成熟负调控因子，功能缺失后，激活成熟相关基因和DML2的表达，促进果实成熟	［60］
非编码RNA	microRNA164A	过表达延缓番茄成熟	［69］
Non-coding RNA	Sly-miR159	靶向赤霉素相关基因，影响果实形状和大小	［70］
	Sly-miR167	抑制生长素响应基因，参与腔室和胎座发育	［71］
	lncRNA1471	结合转录因子ASR，参与果实成熟	［72］

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