Hierarchical chromatin rewiring orchestrates early transcriptional regulation in mouse cerebral cortex following focal ischemia.

Ischemic stroke triggers rapid, spatiotemporally orchestrated transcriptional reprogramming in the brain, yet the mechanisms that confer selective gene expression under acute stress remain poorly understood. Here, we examine how genome architecture dynamically regulates transcription in the peri-infarct cortex following transient middle cerebral artery occlusion (tMCAO). Integrating Hi-C with transcriptomic and cis-regulatory profiling at 6 and 24 h of reperfusion, we show that ischemic injury induces rapid, partially reversible reorganization of chromatin 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 gene programs in the injured cortex. Together, these findings reveal that post-stroke transcriptional reprogramming is constrained by a 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.