3D genome organization in tissue regeneration involves long-range chromatin loops

The three-dimensional (3D) organization of the genome plays a fundamental role in gene expression regulation, yet how changes in genome architecture influence transcriptional responses during tissue regeneration remains poorly understood. Here, we used Hi-C to profile 3D chromatin conformation during Drosophila wing imaginal disc regeneration. We found that, although compartments and topologically associating domains (TADs) are largely maintained, regeneration is accompanied by reduced compartmentalization and decreased boundary insulation. We identified three long-range chromatin loops with increased contact frequency during regeneration. Targeted deletion of their anchors revealed that these loops are essential for proper disc regeneration but dispensable for normal wing development. Furthermore, disruption of any of these loops resulted in convergent changes in both gene expression and H3K4me1 3D environment, suggesting their coordinated activity during regeneration. These findings provide functional evidence that 3D genome architecture actively contributes to the regenerative process.