Three-dimensional chromatin architecture in crustaceans: Emerging evidence, structural principles, and future...

Three-dimensional (3D) chromatin architecture is a fundamental regulatory layer for linking hierarchical chromatin organization to gene expression and phenotypic traits. While spatial genome biology is well-established in vertebrates and some model invertebrates, its application to crustaceans remains comparatively underexplored despite their immense ecological and economic significance. This review provides a comprehensive overview of recent progress regarding hierarchical organization in crustacean 3D architectures. The fundamental structural features, including large-scale chromosome territories, A/B compartments, topologically associating domains (TADs), and chromatin loops, are introduced first. Subsequently, the functional roles of these spatial structures governing essential biological processes, including the ecdysone-mediated molting cycle, metabolic endocrine control, sexual development, and adaptive responses to environmental stress, are summarized. At the end of this review, the unique technical challenges posed by large, highly repetitive crustacean genomes, the modern methodological toolkit of Hi-C, Micro-C, and deep-learning-based data enhancement are discussed. Potential strategies for future functional interrogation of crustacean genomes are offered thereafter. Overall, 3D genomics holds significant potential in crustacean research and is poised to play a pivotal role in advancing sustainable aquaculture, biodiversity conservation, and global food security in rapidly changing ecosystems.