International Journal of Aquaculture, 2025, Vol.15, No.4, 197-207 http://www.aquapublisher.com/index.php/ija 201 4 The Regulatory Effect of Epigenetic Mechanism on Oyster Growth 4.1 DNA methylation and activation or silencing of key growth genes DNA methylation regulates the growth phenotype of oysters by affecting the expression status of growth-related genes. Breeding studies have shown that oyster hybrid offspring often exhibit growth advantages (hybrid dominance), which may be partly attributed to epigenetic regulation. For example, a study on the hybrid offspring of oysters and wild oysters in the "Haida No. 1" breeding line found that the overall DNA methylation level of hybrid oysters is lower than that of the parents, and this genome-wide hypomethylation state may be conducive to the widespread activation of growth-related genes and improve growth rate (Yang and Li, 2022). At the specific gene level, DNA methylation can selectively silen or activate certain growth-critical genes. For example, if the methylation degree of the oyster's growth factors such as BMP, insulin-like growth factors, etc. increases, it will lead to transcriptional repression and hinder growth. Some genes involved in cell cycle and protein synthesis are also regulated by methylation. The study compared the oyster population with different growth rates and found that several growth-related gene promoters in the fast-growing group were demethylated and highly expressed, such as ribosomal protein genes and actin-related genes; while these gene promoters in the slow-growing group were highly methylated and low-expression (Tan et al., 2022). This shows that DNA methylation affects the growth rate of oysters by finely regulating gene expression. In addition to routine development, DNA methylation also plays a role in ploidy breeding. There are often differences in growth traits between long oysters (diploid oysters) and their triploid individuals. Studies have found that there are epigenetic differences in the genomic methylation maps of the two. 4.2 Histone modification regulates nutritional metabolism and energy distribution Oyster growth depends on the accumulation and metabolic efficiency of nutrients, while histone modifications play a regulatory role in it by affecting the expression of metabolic enzymes and related pathway genes. Histone H3 acetylation is usually associated with high transcriptional activity. Under high nutritional conditions, the promoter of the key metabolic enzyme gene in digestive tissues such as oyster hepatitis and pancreas may enrich H3K9 and H3K27 acetylation markers, thereby enhancing the transcription of carbohydrate and lipid metabolic enzymes (Yang et al., 2023). This histone modification-mediated metabolic reprogramming needs to be verified experimentally. On the other hand, the cell proliferation and protein synthesis processes involved in growth are also regulated by histone modification. If the promoter region of genes that promote cell cycle progression is rich in activated histone markers (such as H3K4me3), it is conducive to rapid cell division and accelerated growth; if these genes are silent due to increased inhibitory modifications such as H3K27me3, it may lead to growth stagnation or even dormant state (Figure 1) (Fellous et al., 2019). Oysters often show growth stagnation when they encounter stress because the body preferentially triggers stress defense, and the growth-related genes may be temporarily turned off through histone modification changes. 4.3 Noncoding RNA-mediated regulation of growth signaling pathways Non-coding RNA is also involved in signaling regulation related to oyster growth. In terms of miRNA, many miRNAs promote oyster growth by targeting growth inhibitors or cell cycle regulatory genes. miR-8 is often thought to have a growth-promoting effect in animals, and it may accelerate cell proliferation by inhibiting the translation of certain growth-inhibiting proteins. This type of inference still needs experimental support in oysters (Wang et al., 2021), but preliminary analysis shows that the high expression of oyster miR-8 is positively correlated with shell length growth. In terms of lncRNA, recent studies have shown that some lncRNAs can act as competitive endogenous RNAs, binding to microRNAs to relieve the inhibition of growth genes. An integrated analysis of BMC genomics identified several lncRNAs related to growth regulation in oysters, which are located close to or antisense to important growth genes, such as FAS, CDC42, which encodes the key enzyme of lipid synthesis, and CDC42, which regulates the cytoskeleton (Zhang et al., 2020). The expression of these lncRNAs is induced by culture temperature and bait abundance, and it is presumed that under different culture conditions, it plays a role by influencing the transcription of adjacent growth genes. For example, LNC_012905 is located near the fatty acid synthetase gene, and the expression of both increases under high nutritional conditions, suggesting that the lncRNA may enhance the lipid synthesis pathway and promote the growth of oyster meat.
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