CUX1 SUSTAINS CHROMATIN ACCESSIBILITY AND LONG-TERM HOMEOSTASIS IN L2/3 NEURONS

Survival of cortical neurons is coupled to mechanisms that preserve their identity and functional state, yet these processes remain incompletely understood. CUX1 is a conserved homeobox transcription factor that regulates neuronal identity and connectivity during development. Its large genomic size makes it particularly susceptible to somatic mutations across the neuron’s lifespan.
We used a tamoxifen-inducible conditional knockout strategy to delete Cux1 in somatosensory cortex layer L2/3 neurons at postnatal day 21. Cux1 genomic damage unleashed a defined window of neuronal death at P31, ending at P37 with the loss of nearly 40% of Cux1-deficient neurons. Classical apoptotic markers were absent, while TUNEL labeling increased, indicating a non-apoptotic mechanism. No further neuronal loss was detected after P37, demonstrating a narrow temporal window of vulnerability as well as the capacity of some neurons to reestablish homeostasis.
At P31, neurons exhibited enlarged nuclei and redistribution of DNA toward the nuclear periphery, but this phenotype was recovered in surviving neurons by P37. ATAC-seq of fluorescence-sorted mutant nuclei revealed widespread loss of chromatin accessibility, with further compaction at P37, consistent with a dynamic response-cascade rather than a static change. Behaviorally, Cux1-deficient mice displayed deficits in whisker-dependent sensory discrimination, most significantly at P60 suggesting that the subjacent is affected.
These findings expand Cux1 functions beyond development, establishing it as a key regulator of neuronal homeostasis in the adult cortex, via pioneer-like activity. This developmental mechanism could be highly relevant for age-associated pathological conditions in which neuronal stability progressively declines.