EXPRESS: Hierarchical Chromatin Rewiring Orchestrates Early Transcriptional Regulation in Mouse Cerebral Cortex Following Focal Ischemia

Ischemic stroke triggers rapid, spatiotemporally orchestrated transcriptional reprogramming, yet the mechanisms conferring selective gene expression under acute stress remain poorly understood. Here, we examine how genome architecture dynamically regulates transcription in the peri-infarct cortex following tMCAO. Integrating Hi-C with transcriptomic and cis-regulatory elements at 6h and 24h of reperfusion, we show ischemic injury induces rapid, partially reversible reorganization of compartments, topologically associating domains (TADs), and loops. Although loops are extensively gained, their presence alone does not predict differential gene expression; transcriptional impact depends on concurrent TAD formation. Newly gained TADs act as the principal structural framework for gene regulation, forming insulated domains enriched in enhancers, promoters, and stroke-associated super-enhancers that coordinate both coding and noncoding RNA expression. Unexpectedly, stable B compartments are enriched for upregulated noncoding RNAs, identifying these regions as hubs of injury-responsive transcription. Locus-level analyses, including Bloodlinc and Foxg1, illustrate how coordinated remodeling of loops and TADs sustains or reshapes regulation in the injured cortex. These findings reveal a constrained post-stroke transcriptional reprogramming by hierarchical chromatin architecture in which TAD context constrains loop regulatory output. This “TAD-gated” mechanism provides a framework for understanding selective gene expression and highlights nuclear architecture as a potential regulatory axis in stroke pathophysiology.