Discovery of novel stroke-responsive lncRNAs in the mouse cortex using genome-wide RNA-seq

Long noncoding RNAs (lncRNAs) play major roles in regulating gene expression in mammals, but are poorly understood in ischemic stroke. Using a mouse model of transient focal ischemia, we applied RNA-seq to evaluate for the first time the unbiased, genome-wide expression of lncRNAs as a function of reperfusion time in the cerebral cortex. Focal ischemia was induced in adult male C57BL/6 mice followed by reperfusion for 6, 12 or 24h. Total RNA from ipsilateral cortices was used for Illumina sequencing and reads were mapped to the mouse reference genome (GRCm38). Annotated and novel transcript isoforms were identified and differential expression between the groups was estimated. We observed that the baseline expression of lncRNAs in the healthy cortex was low, but many were highly altered after stroke. Very few of these altered lncRNAs were previously annotated. A total of 259 lncRNA isoforms at 6h, 378 isoforms at 12h, and 217 isoforms at 24h of reperfusion were differentially expressed versus sham controls. Of these, 213, 322 and 171 isoforms at 6, 12 and 24h of reperfusion, respectively, were novel lncRNAs. Reperfusion time-point-specific analyses revealed that the lncRNAs reached peak expression levels at 6h of reperfusion. Positional analysis of ischemia-responsive lncRNAs with respect to ischemia-responsive protein-coding genes identified potential gene-regulatory relationships. Overall, this work shows that transient focal ischemia induces widespread changes in the expression of lncRNAs in the mouse cortex with distinct reperfusion time-point-dependent expression characteristics that may underlie progression of the ischemic pathophysiology. The detection of hundreds of novel ischemia-responsive lncRNAs marks the discovery of new disease-related genomic regions in the adult cortex and may help identify novel opportunities for therapeutic targeting.