• Super-resolution imaging reveals that apparent gaps at common fragile sites are filled with chromatin resembling mitotic nanodomains (MNDs) but lacking compact granules (CGs).
• MiDAS loci at common fragile sites are composed of arrays of MNDs without higher-order CG assembly.
• The absence of CGs at common fragile sites suggests a structural deficiency that may contribute to genomic instability.
• MNDs serve as fundamental building blocks of higher-order chromatin structure, with failure to progress to CGs being a key defect at fragile sites.