Changes in 3D Chromatin Organization Drive Topologically Determined Gene Expression in the Poststroke Mouse Cortex

BACKGROUND: Recent advances in high-throughput transcriptomics have revealed extensive gene expression changes during cerebral ischemia. However, the changes in 3-dimensional chromatin architecture and long-range chromatin looping between genes and distal regulatory elements that drive these gene expression changes remain virtually unexplored. In this study, we map the landscape of the dynamic alterations in topologically associating domains and chromatin loops in the ischemic cortex and evaluate their contributions to poststroke transcriptional changes. METHODS: We used high-throughput chromatin conformation capture (Hi-C) to profile genome-wide changes of the 3-dimensional chromatin architecture in the cerebral cortex of adult mice following a 1-hour middle cerebral artery occlusion and 6 hours of reperfusion or sham treatment. We conducted RNA sequencing to identify the differentially expressed genes that are concomitantly altered in association with the stroke-induced topologically associating domains and loops. RESULTS: We identified 293 altered topologically associating domains following stroke, harboring a total of 60 upregulated differentially expressed genes and 106 downregulated differentially expressed genes. Chromatin looping analysis identified 4323 differentially altered loops in response to stroke, of which 1583 had enriched interactions and 2741 had diminished interactions. These loci included previously unknown enhancer and silencer elements, which were linked to a total of 88 upregulated and 96 downregulated genes. Upregulated genes associated with altered topologically associating domains and loops were linked to endothelial and immune cell functions, suggesting a role for dynamic chromatin remodeling in the poststroke cerebrovascular and neuroimmune response. Conversely, downregulated genes were associated with neuronal and synaptic functions, suggesting a role in poststroke neuronal fate. CONCLUSIONS: This study is the first to map changes in the 3-dimensional chromatin of the adult cerebral cortex following ischemic stroke. Our findings reveal novel regulatory elements directly associated with stroke-altered genes that may be involved in the regulation of these genes via dynamic changes in chromatin architecture and looping characteristics to fine-tune their expression.