1 Introduction

Lycopene is one of the most common carotenoids in the fruit of tomatoes (Solanum lycopersicum). It not only gives the fruit a bright red color, but also is regarded as very important for human health due to its strong antioxidant activity. As the main source of lycopene in human diet, it is closely related to health benefits such as reducing the risk of cardiovascular diseases and some cancers. The accumulation of lycopene is also a key process for fruit ripening and quality formation, which is regulated by many endogenous and exogenous factors (Luo et al., 2013; McQuinn et al., 2017; Ming et al., 2023).

Epigenetics regulates gene expression through heritable means without altering the DNA sequence, including DNA methylation, histone modification, regulation of non-coding RNA, etc. (Wu and Li, 2024). Recent studies have found that these mechanisms play an important role in the development and ripening of tomato fruits. DNA methylation and histone deacetylation can affect the expression of genes related to carotenoid synthesis and regulate the accumulation of lycopene. The research by He et al. (2024) and Nazari et al. (2025) indicates that non-coding RNAs are involved in the regulatory network of fruit ripening and pigment accumulation.

This study summarizes the epigenetic mechanisms regulating lycopene accumulation, introduces the roles of DNA methylation, histone modification, etc. in fruit development and ripening, and reveals how these mechanisms jointly regulate the expression of carotenoid synthesis genes by combining the latest molecular biology and epigenetic research. This study aims to provide a theoretical basis and new methods for precisely regulating lycopene content and improving fruit quality.

2 Lycopene Biosynthesis in Solanum lycopersicum

2.1 Carotenoid biosynthetic pathway: key enzymes and regulation points

Lycopene belongs to the carotenoid family. Its synthetic pathway starts with isoprenyl pyrophosphate (IPP) and is completed through the action of a series of enzymes. The key enzymes include PSY1, PDS, ZDS, ZISO and CRTISO. PSY1 is a rate-limiting enzyme that controls the flow of the entire pathway. CRTISO converts the precursor prolycopene into lycopene. If this enzyme is lacking, prolycopene will accumulate and the fruit will turn orange instead of red (Zhang et al., 2018; Prashanth et al., 2023).

2.2 Genetic determinants influencing lycopene content

Many genes regulate the content of lycopene. In addition to these structural genes, the regulatory gene SlIPT4 (encoding isoprenyltransferase) can positively regulate lycopene synthesis by affecting the expression of ZISO, and has a feedback regulatory effect on ABA (abscisic acid) signaling (Zhang et al., 2018). In addition, the deletion of CRTISO gene function (such as the Tan⁴⁰⁶ mutant) can block the conversion of prolycopene to lycopene, altering the color and nutritional value of the fruit (Prashanth et al., 2023). Transgenic studies have found that exogenous expression of lycopene β-cyclase can significantly increase the content of β-carotene and enhance the flow of the entire carotenoid pathway (Apel and Bock, 2009).

2.3 Developmental and environmental factors affecting accumulation

The accumulation of lycopene can also be influenced by the stage of fruit development and environmental conditions. When the fruit ripens, hormones such as ethylene and jasmonic acid (JA) regulate the expression of related genes and promote the synthesis of lycopene. JA can not only promote lycopene accumulation independently of ethylene, but also restore the lycopene content of JA-deficient mutants through exogenous treatment (Liu et al., 2012). Environmental stresses such as salt stress can inhibit photosynthesis, but at the same time induce the expression of key genes such as PSY1, PDS, ZDS, and LYCB, increase the accumulation of lycopene and other carotenoids, and this effect is specific in different varieties and developmental stages (Leiva-Ampuero et al., 2020).

3 Epigenetic Regulation of Lycopene Biosynthesis

3.1 DNA methylation and transcriptional control of carotenoid genes

DNA methylation is an important mechanism regulating the ripening of tomato fruits and the expression of carotenoid synthesis genes. During the fruit ripening process, the methylation levels in the promoter regions of key carotenoid synthesis genes (such as PSY1, PDS, etc.) undergo dynamic changes, which affect their transcriptional activity and regulate the synthesis and accumulation of lycopene (Ming et al., 2023). Nazari et al. (2025) found that external stresses, such as nanoplastic contamination, can also alter DNA methylation status and indirectly affect lycopene content. DNA methylation also interacts with transcription factors and ethylene signaling pathways to form a complex regulatory network (McQuinn et al., 2017).

3.2 Histone modifications and chromatin remodeling in carotenoid regulation

Histone modification is also crucial in regulating the gene expression of fruit ripening and carotenoid synthesis. After histone deacetylases (such as SlHDA1, SlHDA3, etc.) are silenced, the fruit will ripen more quickly. Histone variants (such as Sl_H2A.Z) directly regulate the expression of key genes such as PSY1 and PDS, and affect the synthesis of lycopene (Figure 1) (Ming et al., 2023; Nazari et al., 2025). Ming et al. (2023) hold that these modifications alter chromatin structure and influence gene accessibility and transcriptional activity, and are one of the core epigenetic mechanisms regulating lycopene accumulation.

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 RNA by RNA m6A 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 from SlDML2, 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 SlMIR164A was involved in negative regulation of tomato fruit ripening (Adopted from Ming et al., 2023)

3.3 Role of microRNAs, lncRNAs, and other non-coding RNAs in post-transcriptional regulation

Non-coding RNAs, especially microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), also play a significant role in the post-transcriptional regulation of fruit ripening and lycopene accumulation. High-throughput sequencing has identified a variety of miRNAs and lncRNAs related to fruit ripening, which affect lycopene accumulation by regulating the mRNA stability and translation efficiency of carotenoid synthesis genes (Ming et al., 2023). In their 2018 study, Chen et al. found that miR1916 can regulate the expression of transcription factors and related enzymes, indirectly affecting the accumulation of secondary metabolites, indicating that miRNA may play a key role in regulating the synthesis of lycopene and other pigments.

4 Interaction Between Epigenetic Modifications and Environmental Cues

4.1 Temperature, light, and stress effects on epigenetic regulation

Environmental factors can affect the ripening of tomato fruits and the accumulation of lycopene through epigenetic mechanisms. Light regulates the synthesis of lycopene through phytochromes in fruits. Alba et al. (2000) found in their early research that red light treatment could significantly promote the accumulation of lycopene in tomato fruits, while far-red light would reverse this effect, indicating that photosensitive pigments are 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).

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.

5 Case Study: Epigenetic Mechanisms in High-Lycopene Tomato Cultivars

5.1 Selection of contrasting tomato cultivars for analysis

When studying the epigenetic regulation of lycopene accumulation, comparison varieties with high lycopene and low lycopene are usually selected. These varieties have significant differences in lycopene content during the fruit ripening process and are very suitable for studying the differences in epigenetic regulation. The commonly used varieties include ‘MicroTom’, ‘Ailsa Craig’ and their mutants. The lycopene content and the expression of related genes of these varieties show significant differences at the fruit development and ripening stages (Ming et al., 2023; He et al., 2024).

5.2 Experimental methods: methylation mapping, transcriptome profiling

To systematically study epigenetic mechanisms, researchers usually employ high-throughput technologies such as whole-genome DNA methylation sequencing (WGBS) and transcriptome sequencing (RNA-seq). Methylation profiling analysis can determine the methylation status of the promoter regions of genes related to lycopene synthesis and reveal the regulatory role of DNA methylation on gene expression. Transcriptome analysis is used to compare the expression levels of key genes in the lycopene synthesis pathway under different varieties or different treatment conditions. Histone modifications and the expression of non-coding RNAs were also detected by methods such as ChIP-seq and small RNA sequencing (Ming et al., 2023; He et al., 2024).

5.3 Key findings on epigenetic marks correlating with lycopene levels

Research has found that in high-lycopene varieties, the DNA methylation levels in the promoter regions of key lycopene synthesis genes (such as PSY1, PDS, etc.) are significantly reduced. This will enable these genes to be expressed at high levels, thereby promoting the accumulation of lycopene. In addition, histone deacetylases (such as SlHDA1 and SlHDA3) and histone variants (such as Sl_H2A.Z) also play significant roles in the expression of related genes. Their expression or modification state changes are closely related to the content of lycopene (Ming et al., 2023). Members of the AP2 family of transcription factors (such as SlAP2c and SlAP2a) regulate histone acetylation levels and directly affect the expression of lycopene synthesis genes, thereby controlling lycopene accumulation in fruits (He et al., 2024). In addition, environmental stress, such as exposure to nanoplastics, can also indirectly affect lycopene content by altering DNA methylation and histone modification (Nazari et al., 2025).

6 Biotechnological and Breeding Applications

6.1 Epigenome editing tools: CRISPR/dCas9-based epigenetic regulation

The CRISPR/dCas9 system can link inactivated Cas9 (dCas9) to epigenetic modification enzymes, such as DNA methyltransferases, demethylases or histone acetyltransferases. In this way, DNA methylation, demethylation or histone modification can be achieved at specific locations, thereby precisely controlling the expression of target genes (Figure 2) (Pan et al., 2021; Cai et al., 2023). For instance, dCas9 can bind to transcriptional activators (such as VP64, p300) or inhibitors (such as KRAB, DNMT3A), respectively activating the gene (CRISPRa) or silencing it (CRISPRi) This method can be used to regulate the key genes related to lycopene synthesis (Moradpour and Abdulah, 2019; Jogam et al., 2022). Furthermore, the CRISPR/dCas9 platform can simultaneously regulate multiple genes and even alter chromatin structure, providing a powerful tool for precisely controlling the lycopene metabolic pathway (Moradpour and Abdulah, 2019).

Figure 2  Schematic of the CRISPR/dCas9 regulatory target gene (Adopted from Cai et al., 2023) Image caption: The expression vector expresses the dCas9 fusion protein in cells, which binds the transcribed sgRNA to form the CRISPR/dCas9 regulatory tool, resulting in the recruitment of the effector domain to the promoter or enhancer region of the target gene under the guidance of sgRNA. Effector domains act on promoters or enhancers of target genes to modify these regions, regulating target gene expression (Adopted from Cai et al., 2023)

6.2 Marker-assisted and epigenetic breeding strategies for lycopene enhancement

The combination of molecular marker-assisted selection (MAS) and epigenetic markers can accelerate the genetic improvement of traits related to lycopene content. Tiwari et al. (2023) found that through genome-wide association study (GWAS) and epigenomic sequencing, epigenetic variations closely related to lycopene accumulation could be identified, and then efficient molecular markers could be developed for breeding screening. Genome editing technologies such as CRISPR/Cas9 and CRISPR/dCas9 can directly act on the key genes in the lycopene synthesis pathway to achieve rapid and precise trait improvement (Chandrasekaran et al., 2021; Tan et al., 2024).

6.3 Potential for integrating epigenomic data into tomato improvement programs

With the development of high-throughput epigenomic sequencing technology, integrating multi-faceted epigenetic data such as DNA methylation, histone modification and non-coding RNA can more comprehensively analyze the regulatory network of lycopene accumulation (Moradpour and Abdulah, 2019). Combining epigenomic information with traditional genotype and phenotypic data can establish more accurate trait prediction models to assist in tomato variety improvement decisions (Karlson et al., 2021; Tiwari et al., 2023). In the future, the integration of epigenomic data is expected to promote molecular design breeding of lycopene high accumulation varieties and achieve targeted improvement of nutritional quality (Moradpour and Abdulah, 2019; Karlson et al., 2021).

7 Research Gaps and Future Perspectives

7.1 Limitations in current epigenomic studies on tomato carotenoids

At present, there are still many deficiencies in the research on the epigenetic regulation of tomato carotenoids, especially lycopene. Although mechanisms such as DNA methylation, histone modification and non-coding RNA have been demonstrated to be related to fruit ripening and metabolic pathways, a complete regulatory network targeting key genes for lycopene synthesis has not been established, and systematic identification of related regulatory factors is also insufficient (Ming et al., 2023). Many studies only focus on a single epigenetic level and fail to delve into the interactions among different epigenetic modifications and their comprehensive regulatory effects on the entire carotenoid metabolic pathway. The mechanism by which environmental stress affects the epigenetic status and lycopene accumulation of tomatoes has not been systematically studied yet (Nazari et al., 2025).

7.2 Multi-omics approaches for integrative understanding

Multi-omics integration is an important future direction for solving these problems. The combination of data from genomics, epigenomics, transcriptomics, metabolomics, etc. can be used to analyze the dynamic relationship among epigenetic modifications, gene expression and metabolite accumulation. The histone variant Sl_H2A.Z has been proven to regulate the expression of genes related to carotenoid synthesis (Ming et al., 2023), but its synergistic effects with mechanisms such as DNA methylation and non-coding RNA still require multi-omics data for explanation. The influence of epigenetic changes caused by environmental factors on lycopene accumulation can be tracked and analyzed by multi-omics methods (Nazari et al., 2025).

7.3 Prospects for precision agriculture and metabolic engineering

With the continuous revelation of epigenetic regulatory mechanisms, precision agriculture and metabolic engineering will have great potential in the targeted regulation of lycopene. By regulating key epigenetic factors, it is possible to achieve precise control of the lycopene synthesis pathway and improve the nutritional quality of fruits (Ming et al., 2023). Molecular breeding and gene editing technologies based on epigenetic markers will also provide new theoretical foundations and technical support for the breeding of varieties with high lycopene content. In the future, it is necessary to study the plasticity of epigenetic regulation under environmental stress to improve the stress adaptability and fruit quality of tomatoes (Nazari et al., 2025).

Acknowledgments

The authors thank Professor Gai for his meticulous guidance and valuable modification suggestions during the process of writing the manuscript of this study.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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