This study investigates the multiscale 3D genome reorganization during mouse neural development using ultra-deep Hi-C data from in vitro and in vivo neural differentiation. The research reveals that transcription is correlated with chromatin insulation but is not sufficient to create TAD boundaries de novo. The study identifies dynamic contacts between gene bodies, enhancer-promoters, and transcription factor (TF) sites during neural differentiation. It shows that the Polycomb network is disrupted, while novel TF interactions emerge. The 3D genome undergoes global reorganization, with a progressive increase in compartment size, decreased interactions within the A compartment, and increased interactions between B-type domains. Transcription is correlated with chromatin insulation but is not sufficient to induce insulation at TAD boundaries. Dynamic CTCF-based loops and insulation are observed during neural differentiation. Active gene promoters and exon-rich gene bodies interact at multiple genomic scales. Polycomb-mediated interactions are disrupted during neural differentiation, while cell-type-specific enhancer-promoter contacts are established concomitant with gene expression. The study highlights the importance of multiple factors in shaping dynamic chromatin interactions during development, providing insights into the relationship between genome architecture and gene expression. The findings suggest that chromatin interactions are highly dynamic and cell-type specific, with enhancer-promoter interactions often occurring during gene expression. The study also identifies that gene bodies of highly expressed genes interact strongly both in cis and trans, forming clusters of loops. These interactions are strongly correlated with the number of splicing events per gene. The research provides a comprehensive view of chromatin organization, showing that different regulatory factors establish preferential contacts at different scales, ranging from close cis interactions to long-range TAD-delimited contacts and very long-range contacts involving promoters, Polycomb, heterochromatin regions, and a subset of TF binding sites. The study underscores the importance of dynamic chromatin looping in gene activation and cell fate determination.This study investigates the multiscale 3D genome reorganization during mouse neural development using ultra-deep Hi-C data from in vitro and in vivo neural differentiation. The research reveals that transcription is correlated with chromatin insulation but is not sufficient to create TAD boundaries de novo. The study identifies dynamic contacts between gene bodies, enhancer-promoters, and transcription factor (TF) sites during neural differentiation. It shows that the Polycomb network is disrupted, while novel TF interactions emerge. The 3D genome undergoes global reorganization, with a progressive increase in compartment size, decreased interactions within the A compartment, and increased interactions between B-type domains. Transcription is correlated with chromatin insulation but is not sufficient to induce insulation at TAD boundaries. Dynamic CTCF-based loops and insulation are observed during neural differentiation. Active gene promoters and exon-rich gene bodies interact at multiple genomic scales. Polycomb-mediated interactions are disrupted during neural differentiation, while cell-type-specific enhancer-promoter contacts are established concomitant with gene expression. The study highlights the importance of multiple factors in shaping dynamic chromatin interactions during development, providing insights into the relationship between genome architecture and gene expression. The findings suggest that chromatin interactions are highly dynamic and cell-type specific, with enhancer-promoter interactions often occurring during gene expression. The study also identifies that gene bodies of highly expressed genes interact strongly both in cis and trans, forming clusters of loops. These interactions are strongly correlated with the number of splicing events per gene. The research provides a comprehensive view of chromatin organization, showing that different regulatory factors establish preferential contacts at different scales, ranging from close cis interactions to long-range TAD-delimited contacts and very long-range contacts involving promoters, Polycomb, heterochromatin regions, and a subset of TF binding sites. The study underscores the importance of dynamic chromatin looping in gene activation and cell fate determination.