Chromatin Packing Domain Engineering Through the Manipulation of Nuclear Cationic States

Cells must preserve and rewrite transcriptional memory to maintain identity and adapt to stress, yet the physical mechanisms governing this process remain unclear. Recent work implicates genome geometry in encoding transcriptional memory, with nanoscopic chromatin packing domains (PDs) serving as structural units that stabilize or reprogram transcriptional states. One powerful, yet underexplored regulator of this architecture is the nuclear ionic environment. Divalent cations can stabilize PDs through charge screening and phosphate bridging, suggesting a direct physicochemical mechanism linking ions to genome organization. In this study, we show that manipulating nuclear divalent cations is sufficient to reshape chromatin architecture, transcriptional output, and cellular resilience in living human cancer cells. Selective cation depletion (BAPTA-AM, APDAP-AM) produces smaller, less compact PDs and diminishes H3K9me3-enriched heterochromatic cores, structural anchors of transcriptional memory. In contrast, magnesium enrichment enhances packing density and domain maturation. Live-cell nanoscopy reveals that chromatin packing scaling responds within minutes to ionic perturbation. Transcriptomic profiling demonstrates coordinated gene expression changes and reduced adaptive plasticity, while chelator pretreatment increases chemotherapy sensitivity. Together, these findings identify nuclear ions as rapid, reversible regulators of chromatin packing domains and transcriptional memory, revealing ionic homeostasis as a fundamental mechanism linking genome architecture to cellular adaptation.