This study investigates the role of cohesin in chromosomal organization and its impact on gene expression. The authors deleted the *Nipbl* gene, which encodes a cohesin-loading factor, in mouse liver cells using a liver-specific, tamoxifen-inducible Cre driver. Depletion of cohesin led to a dramatic reorganization of chromosomal folding, with the disappearance of topological domains (TADs) and associated peaks, while compartmental segregation was preserved and even reinforced. Notably, the disappearance of TADs revealed a finer compartment structure that accurately reflects the underlying epigenetic landscape. The findings suggest that 3D genome organization results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments defined by chromatin state, and cohesin-dependent formation of TADs, possibly through loop extrusion. The study also highlights the importance of cohesin in maintaining long-range regulatory interactions and the potential role of cohesin in initiating changes in gene expression driven by distant enhancers.This study investigates the role of cohesin in chromosomal organization and its impact on gene expression. The authors deleted the *Nipbl* gene, which encodes a cohesin-loading factor, in mouse liver cells using a liver-specific, tamoxifen-inducible Cre driver. Depletion of cohesin led to a dramatic reorganization of chromosomal folding, with the disappearance of topological domains (TADs) and associated peaks, while compartmental segregation was preserved and even reinforced. Notably, the disappearance of TADs revealed a finer compartment structure that accurately reflects the underlying epigenetic landscape. The findings suggest that 3D genome organization results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments defined by chromatin state, and cohesin-dependent formation of TADs, possibly through loop extrusion. The study also highlights the importance of cohesin in maintaining long-range regulatory interactions and the potential role of cohesin in initiating changes in gene expression driven by distant enhancers.