International Journal of Aquaculture, 2025, Vol.15, No.4, 197-207 http://www.aquapublisher.com/index.php/ija 199 stress resistance. For example, experimental comparisons found that the survival rate of "Haida No. 1" breeding oysters that grew rapidly during the same period under low salt and high temperature stress was lower than that of slower-growing wild populations, showing a potential balance mechanism between growth and tolerance (Li et al., 2022). In addition, growth and retardation also affect each other through endocrine and signaling pathways. For example, nutrition and growth-related insulin signaling pathways and the KEAP1-Nrf2 pathway that responds to antioxidant stress may cross at the energy metabolism node. When environmental stress activates Nrf2-mediated antioxidant genes, it may inhibit the growth metabolic pathway of oysters to ensure survival priority. In essence, the trade-off between growth and stress resistance reflects the balance between biological resource allocation and survival and reproduction strategies. Understanding the genetic and epigenetic basis of this balance will help to simultaneously optimize oyster growth rate and environmental adaptability in breeding. 3 Main Types of Epigenetic Regulation of Oysters 3.1 DNA methylation and its role in gene expression regulation DNA methylation is one of the most studied mechanisms in the epigenetic regulation of oysters. Typical mosaic methylation distributions exist in the oyster genome: the accumulation of 5-methylcytosine (5mC) can be detected in the gene coding region and promoter region, while the vast majority of non-CpG regions remain unmethylated. High-throughput sequencing analysis estimated that approximately 1.8% of cytosines in the entire genome of Pacific oysters had methylation modification. This methylation level is much lower than that of mammals, but is comparable to other invertebrates (such as insects). Oyster DNA methylation mainly occurs on CpG dinucleotides, showing a pattern of hypermethylation of gene bodies and hypomethylation of promoters. This methylation pattern is thought to be associated with constitutive and inducible expression characteristics of the gene. DNA methylation is generally regarded as a transcriptional repression signal: When the CpG island on the gene promoter is highly methylated, methylated binding proteins and chromatin remodeling complexes are recruited, making the local chromatin appear tightly, thereby inhibiting the binding of transcription factors and reducing gene expression (Li et al., 2024). In contrast, promoter demethylation is often associated with gene activation. 3.2 Regulatory functions of histone modification and chromatin remodeling Covalent modification of histones is another important aspect of epigenetic regulation. In invertebrates such as oysters, although histone modification research is relatively limited, the conservative histone modification mechanism also exists in their genome. The lysine residues at the N-terminal tail of histones can undergo various modifications, including methylation, acetylation, ubiquitination, phosphorylation, etc. These chemical tags change the conformation of chromatin and thus affect transcriptional activity. For example, trimethylation of histone H3 lysine 4 (H3K4me3) is usually associated with transcriptional initiation activity, while H3K27me3, as a classic marker of transcriptional repression, is associated with gene silencing and pluripotency maintenance. There are also enzymes in the oyster genome that regulate these histone modification states, such as histone methyltransferase and demethylase, acetyltransferase (HAT) and deacetylase (HDAC). A class of homologs of lysine-specific histone demethylase 1 (LSD1) containing typical SWIRM domains and amine oxidase domains were identified in Pacific oysters. Functional studies show that after knocking down the Oyster LSD1 gene, the two activity-related markers H3K4me1 and H3K4me2 are significantly increased in blood cells and are accompanied by upregulation of the hemocytic proliferation rate (Fellous et al., 2019). This means that LSD1 maintains the normal proliferation rhythm during oyster blood cell development by removing methyl groups on H3K4. In addition, when stimulated by bacteria, the transcription level of Oyster LSD1 rapidly declines, allowing the promoters of more immune-related genes to retain H3K4 methylation activity markers, thereby promoting the differentiation and release of antibacterial cells. This discovery reveals the mechanism by which histone demethylase regulates oyster immune function through chromatin state. 3.3 The role of non-coding RNA in regulatory networks 3.3.1 Research on miRNA-mediated inhibition of target gene expression and function MiRNA is a small RNA about 20 to 24 nucleotides in length and can be paired with the 3’ untranslated region of the target mRNA, thereby triggering mRNA degradation or inhibiting translation. Hundreds of miRNA molecules
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