Deciphering the 3D structures of plant genomes: building blocks of hierarchically organized chromatin domains

The spatial arrangement of chromatin within the nucleus is intricately regulated and acts as a key determinant of gene expression. Advanced high-resolution chromatin conformation capture techniques have revealed that plant genomes exhibit hierarchical organization within the nucleus into large compartments, intermediate topologically associating domain (TAD)-like domains, and fine gene-scale chromatin domains. In this review, we highlight recent findings demonstrating that TAD-like domains are closely associated with distinct epigenetic states, modulated by cohesin components. In addition, we underscore the significance of gene-scale chromatin domains, which are established by RNA polymerase II and accessible chromatin structures at gene borders. These fine-scale chromatin domains likely serve as the fundamental structural units for higher-order chromatin organization. Examining the chromatin structures at different levels of the hierarchy allows us to elucidate their epigenetic features and the molecular mechanisms for domain formation, providing insights into the three-dimensional organization of plant genomes.