Super-resolution imaging reveals higher-order structures within common fragile sites in human mitotic chromosomes

• Super-resolution imaging reveals that apparent gaps at common fragile sites (CFSs) are filled with chromatin resembling mitotic nanodomains (MNDs) but lacking compact granules (CGs). • Mitotic DNA synthesis (MiDAS) loci exhibit only MND-level organization, indicating a structural deficiency in higher-order chromatin assembly at CFSs. • This study provides the first ultrastructural characterization of CFSs and MiDAS loci, linking replication stress to specific chromatin architecture defects. • The findings suggest that failure to progress from MNDs to CGs may underlie genomic instability at CFSs, offering new insights into carcinogenesis and developmental disorders.