Analysis of long non-coding RNA expression profiles following focal cerebral ischemia in mice

Long noncoding RNAs (lncRNAs) have a variety of biological functions and play key roles in many diseases. However, the knowledge of lncRNA function during a stroke is limited. We analyzed the expression profiles of lncRNAs in the brain ischemic region of mice after a 45 min middle cerebral artery occlusion (MCAO) with a 48 h reperfusion. Gene ontology and pathway analysis were used to elucidate the potential functions of the differentially expressed mRNAs. A total of 255 lncRNAs (217 up-regulated and 38 down-regulated) and 894 mRNAs (870 up-regulated and 24 down-regulated) showed significantly altered expression in the ischemic brain compared to the sham controls (fold change ≫>2, P ≪ 0.05). The gene ontology terms were mainly associated with neutrophil chemotaxis, positive regulation of inflammatory response, cell cycle, positive regulation of apoptotic process, and apoptotic process. The pathway analysis indicated that the mRNAs were mainly associated with inflammatory pathways. Additionally, the interactions between the differentially expressed lncRNAs and mRNAs are revealed by a dynamic lncRNA-mRNA network. Our findings provide an overview of aberrantly expressed lncRNAs in stroke and further broaden the understanding of stroke pathogenesis.