The Divergent 3D Genome Landscapes of Aging and Neurodegenerative mouse models

Chromatin structure is essential for gene regulation and genome stability, and neurons must preserve their 3D genome organization throughout life. This structure gradually deteriorates with aging and is further disrupted in neurodegenerative diseases. To investigate whether aging and neurodegeneration share early chromatin changes or diverge, we performed Hi-C on cortical neurons from adult, aged, and brain-specific SIRT6-knockout (S6-KO) mice, and compared them to the CK-p25 Alzheimer’s disease model results stratified by γH2AX levels. All models showed early features such as weakened interactions between chromosomes in expanded nuclei, A-to-B compartment shifts, and loss of architectural loops. However, aged neurons retained TAD prominence, short-range interactions, and enhancer-promoter loops, while pathological models showed reduced TAD prominence, shorter loops, and disorganized A–B mixing. These changes correlate with increased DNA damage. Our findings suggest that aging represents a “primed” state, where chromatin regulation begins to erode, but further stressors like DNA damage are associated with progression toward neurodegenerative breakdown.