The genome is a highly complex and dynamic environment whose precise organization is essential for a wide range of cellular functions, including chromosomal integrity, DNA replication, genome maintenance, and transcriptional regulation. Genome organization is inherently multi-scale, encompassing hierarchical structures that range from the organization of individual nucleosomes and chromatin fibers to the formation of higher-order domains, nuclear compartments, and interactions spanning multiple chromosomes. Increasing evidence also suggests that the spatial organization of the genome is closely coupled to the biophysical properties of chromatin and its associated factors.

In particular, liquid–liquid phase separation and related biomolecular condensation mechanisms have emerged as important principles through which chromatin and chromatin-associated proteins can dynamically organize nuclear components and regulate their local biochemical environments. Together, these findings highlight the need for standardized and quantitative frameworks capable of probing genome organization across multiple spatial and temporal scales.

This Topical Collection aims to present innovative methodologies, conceptual frameworks, and computational tools that leverage recent advances in the study of genome organization. Given the inherently multidisciplinary nature of this field, progress increasingly depends on integrating approaches from molecular and cell biology, biophysics, bioengineering, microscopy, genomics, and data science. Such integration can provide complementary perspectives on how genomic information is physically organized, how this organization changes across cellular states, and how genome architecture influences genome function.

By bringing together emerging experimental and computational approaches, this collection seeks to provide a practical framework for investigating the principles, mechanisms, and functional consequences of genome organization across scales.