65 / 2026-04-04 14:53:34

3D genome reorganization associated with nuclear remodeling during alveolar epithelial cell fate transition

alveolar epithelial cell,droplet Paired&Tag

The transdifferentiation of alveolar type II (AT2) into type I (AT1) epithelial cells is accompanied by pronounced nuclear flattening; however, how such morphological changes are manifested in the three-dimensional (3D) genome across distinct spatial scales remains poorly understood. Here, we integrate multi-omics approaches to systematically characterize 3D genome organization in alveolar epithelial cells under both homeostatic and injury-induced regenerative conditions. Under homeostasis, AT1 cells exhibit extensive reorganization of chromatin architecture relative to AT2 cells, with clear hierarchical features. Compartmentalization is globally weakened, a subset of regions undergo compartment state changes, and intra-TAD interactions are reduced. Notably, chromatin loops display the most pronounced alterations, with a global reduction in loop numbers, indicating a reconfiguration of long-range regulatory interactions during terminal differentiation. During injury-induced regeneration, these structural features display distinct layer-specific dynamics. Compartment- and TAD-level organization progressively converge toward an AT1-like state with relatively limited magnitude of change, whereas chromatin loops undergo more prominent, stage-specific remodeling. A large number of injury-associated loops emerge that are distinct from both steady-state AT2 and AT1 configurations and are preferentially enriched at genes involved in epithelial differentiation and Hippo signaling. Integration with single-cell Droplet Paired&Tag data further reveals that a subset of these injury-associated loops is concordant with cell-type–specific enhancer–gene linkages in transitional cell populations, supporting a relationship between long-range chromatin interactions and transcriptional changes at single-cell resolution. Collectively, our results delineate a hierarchical principle of 3D genome remodeling during cell fate transition, in which global topological features undergo gradual adjustment, whereas local chromatin interactions serve as the primary layer of dynamic regulatory modulation, providing a spatial framework for understanding gene regulation under structural constraints.