Tree Genetics and Molecular Breeding 2025, Vol.15, No.3, 128-137 http://genbreedpublisher.com/index.php/tgmb 130 3 Epigenetic Regulation in Plants 3.1 DNA methylation: types, functions, and measurement DNA methylation is one of the most important mechanisms in the epigenetic regulation of plants. It mainly occurs on the two bases of cytosine (C) and adenine (A). Methylation often occurs in the CG, CHG and CHH sequences (where H stands for A, T or C). It can prevent genes from being transcribed, thereby affecting gene expression and transposon activity (Liang et al., 2019). The changes in DNA methylation are regulated by two types of enzymes: methyltransferases are responsible for adding methyl groups, while demethylases remove them. This change is reversible (Chang et al., 2019; Tresas et al., 2025). DNA methylation often plays a key role during plant development, environmental adaptation or coping with adverse conditions (Abdulraheem et al., 2024). At present, researchers usually use some techniques to detect DNA methylation, such as methylation-sensitive digestion, methylation-specific PCR, and whole-genome methylation sequencing (Liang et al., 2019; Da Costa et al., 2024). 3.2 Histone modifications and chromatin remodeling in gene expression In addition to DNA methylation, histone modification is also an important regulatory approach. It includes types such as methylation, acetylation and ubiquitination. These modifications are like a kind of “code” that can change the structure of chromatin and thereby affect whether genes are activated. For instance, methylation on H3K4 and H3K36 often makes genes more easily expressed, while methylation on H3K9 and H3K27 may silence genes (Xu et al., 2018). The activities of these modification enzymes can also be affected by the external environment or intracellular metabolism, thereby helping plants respond quickly to stress and even generate “memory” responses (Kumar et al., 2020). Furthermore, chromatin remodeling complexes can further affect whether genes are easily readable by moving the position of nucleosomes or changing their number (Tresas et al., 2025). 3.3 Non-coding RNAs and their roles in epigenetic signaling Non-coding RNAs (ncRNAs) also play a significant role in epigenetic regulation. They include small interfering RNA (siRNA) and microRNA (miRNA), etc. siRNA can guide DNA methylation or silence certain genes after transcription, which can prevent transposon activity and also regulate gene expression (Ramirez-Prado et al., 2018). miRNA participates in regulating development and response to stress by cutting mRNA or blocking protein translation (Xu et al., 2018). These non-coding RNAs often work together with DNA methylation and histone modification to construct a complex regulatory network. 4 Environmental Effects on Epigenetic Marks 4.1 Altitude-related environmental changes: temperature, UV, and oxygen availability The increase in altitude brings about some environmental pressures, such as lower temperatures, stronger ultraviolet rays, and less oxygen in the air. These changes can induce epigenetic modifications in the plant genome, such as DNA methylation and histone modifications. These modifications can regulate gene expression and help plants adapt to new environments (Baduel et al., 2024; Bogan and Yi, 2024). For instance, temperature changes can regulate gene activity by influencing the structure of chromatin. Ultraviolet rays may cause DNA damage, thereby bringing about epigenetic changes. And changes in oxygen concentration can also regulate genes related to REDOX (Varotto et al., 2020; Ali et al., 2022). These changes enable plants like Camellia oleifera to exhibit different traits at different altitudes and survive better (Miryeganeh, 2021; Bogan and Yi, 2024). 4.2 Stress-induced epigenetic responses in perennial woody plants For perennial woody plants like Camellia oleifera, in the face of repeated or long-term stresses such as drought, low temperature and strong light, they will also regulate the expression of related genes by means such as DNA methylation, histone acetylation or methylation (Ali et al., 2022; Bogan and Yi, 2024). These changes not only enable plants to respond quickly to the environment, but also allow them to “remember” these stresses. When plants encounter similar conditions again, they can react faster and more effectively (He and Li, 2018; Baduel et al., 2024). This mechanism is more flexible than gene mutations, enabling plants to adapt more easily to complex environments and facilitating long-term survival (Varotto et al., 2020; Miryeganeh, 2021). 4.3 Transgenerational epigenetic memory and adaptation potential Some epigenetic markers caused by the environment do not only function within a single plant but can also be
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