Rewiring of the three-dimensional genome encodes regenerative potential in the adult central nervous system

Abstract The failure of adult central nervous system neurons to regenerate after injury has been attributed to transcriptional and epigenetic barriers, but whether three-dimensional genome organization constitutes an independent regulatory layer encoding regenerative potential remains unknown. Here we present the first genome-wide map of chromatin compartments, topologically associating domains, and loops across postnatal development, adult homeostasis, and spinal cord injury in the mouse motor cortex. Postnatal maturation progressively consolidates a growth-restrictive three-dimensional architecture, and spinal cord injury alone partially reverses this consolidation, re-engaging neonatal gene programs through reorganized but functionally recapitulative architecture despite minimal transcriptional activation. This reversion is directed rather than stochastic, preferentially targeting pro-growth gene networks, and reveals a latent three-dimensional memory of developmental growth states in the adult cortical genome. Strikingly, NR2F6, a transcription factor that promotes corticospinal axon regeneration, extends this reversion beyond the neonatal state toward an earlier embryonic chromatin configuration, a depth of developmental plasticity that injury alone cannot reach. These findings establish three-dimensional genome topology as a regulatory layer encoding regenerative potential in adult cortical neurons, demonstrating that successful CNS regeneration requires accessing embryonic rather than merely neonatal chromatin states, and reframing regenerative failure as a topological problem with new therapeutic targets.