Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse

Cell differentiation is a complex process characterized by specific gene expression patterns regulated through enhancer-promoter interactions within the three-dimensional architecture of the nucleus. The precise role of cohesin loading dynamics in restructuring chromatin during pancreatic lineage commitment remains unclear. Here we show that knockdown of cohesin loader NIPBL disrupts enhancer-promoter interactions and CTCF-mediated loops, leading to widespread transcriptional dysregulation. Furthermore, the loss of cohesin-mediated loops is accompanied by increased contacts between Polycomb Repressive Complex (PRC) domains, highlighting the interplay between cohesin dynamics and PRC-mediated compartmentalization. Although RAD21 and SA1 cohesin levels remain stable at CTCF loop anchors, NIPBL is essential for maintaining long-range chromatin interactions at later differentiation stages. These findings establish cohesin loading as a critical regulator of 3D genome reorganization during cell fate determination, providing a mechanistic framework for understanding cohesinopathy-related developmental disorders. NIPBL knockdown in human pancreatic differentiation reveals that cohesin loading is essential for enhancer-promoter connectivity and CTCF loop maintenance, while its loss drives Polycomb domain. compaction and impairs stage-specific genome folding.