Bioinformatics analysis of a long non-coding RNA and mRNA regulation network in rats with middle cerebral artery occlusion based on RNA sequencing

Long non-coding RNAs (lncRNAs) have been proven to be critical gene regulators of development and disease. The main aim of the present study was to elucidate the lncRNA-mRNA regulation network in ischemic stroke induced by middle cerebral artery occlusion (MCAO) using RNA sequencing (RNA-seq) in rats. lncRNA expression profiles were screened in brain tissues to identify a number of differentially expressed lncRNAs (DELs) and genes (DEGs) by RNA-seq. Reverse transcription-quantitative polymerase chain reaction was performed to further confirm the lncRNA expression data. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to mine mRNA functions, and a lncRNA-mRNA network was constructed. Additionally, cis- and trans-regulatory gene analyses of DELs were predicted. A total of 134 DELs (fold change >2, false discovery rate <0.05) and 1,006 DEGs (fold change >2 and P<0.05) were identified. Eighteen lncRNAs were predicted to regulate heme oxygenase 1, mitotic checkpoint serine/threonine kinase B, chemokine ligand 2 and DNA Topoisomerase IIα, amongst other genes. These genes are all associated with a cellular response to inorganic substances, alkaloids, estradiol, reactive oxygen species, metal ions, oxidative stress, and are associated with metabolic pathways, chemokine signaling pathways, malaria, Parkinson's disease, the cell cycle and other GO and KEGG pathway enrichments. The present study identifies novel DELs and an lncRNA-mRNA regulatory network that may allow for an improved understanding of the molecular mechanism of ischemic stroke induced by MCAO.