Effect of Focal Ischemia on Long Noncoding RNAs

Abstract

Background and Purpose— Long noncoding RNAs (lncRNAs) play a significant role in cellular physiology. We evaluated the effect of focal ischemia on the expression of 8314 lncRNAs in rat cerebral cortex using microarrays. Methods— Ischemia was induced by transient middle cerebral artery occlusion. Genomic and transcriptomic correlates of the stroke-responsive lncRNAs and the transcription factor binding sties in their promoters were evaluated with bioinformatics. Results— Three hundred fifty-nine lncRNAs were upregulated (>2-fold) and 84 were downregulated (<0.5-fold) at 3 hours to 12 hours of reperfusion after middle cerebral artery occlusion compared with sham. Sixty-two stroke-responsive lncRNAs showed >90% sequence homology with exons of protein-coding genes. Promoters of stroke-responsive lncRNA genes and their homologous protein-coding genes showed highly overlapping transcription factor binding sites. Despite presence of open reading frames, lncRNAs did not form any product when subjected to in vitro translation. Conclusions— Stroke significantly alters cerebral lncRNA expression profiles.