Fish Epigenetics: Molecular Mechanisms, Environmental Adaptation, and Emerging Computational Approaches

Epigenetic regulation has transformed our understanding of how fish adapt to changing environments by modulating gene expression without altering the underlying DNA sequence. This review explores the “dark mastery” of fish epigenetics by providing mechanistic insights into the principal epigenetic processes, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs, that govern development, immunity, stress responses, and disease susceptibility. These regulatory mechanisms enable fish to respond dynamically to environmental stressors such as temperature fluctuations, salinity shifts, hypoxia, pollutants, ultraviolet radiation, and nutritional changes, thereby influencing physiological resilience, reproductive performance, and survival. Recent advances in next-generation sequencing and multi-omics technologies have substantially expanded our understanding of the fish epigenome, while bioinformatics has become indispensable for integrating and interpreting complex genomic, transcriptomic, and epigenomic datasets. Furthermore, artificial intelligence (AI) and machine learning (ML) are emerging as powerful approaches for biomarker discovery, predictive modeling of disease susceptibility, environmental risk assessment, and precision aquaculture. The integration of epigenetics with bioinformatics and AI provides unprecedented opportunities to decipher complex regulatory networks, identify adaptive epigenetic signatures, and develop data-driven strategies for improving fish health and aquaculture sustainability. Despite these advances, important challenges remain, including limited species-specific epigenomic resources, difficulties in multi-omics integration, model interpretability, and the need for standardized analytical frameworks. This review highlights current knowledge, emerging computational approaches, and future perspectives for translating epigenetic discoveries into sustainable aquaculture practices and aquatic ecosystem conservation under accelerating environmental change.