Altered expression of long non-coding RNA and mRNA in mouse cortex after traumatic brain injury

Abstract Background and objective The present study aims to detect the altered lncRNA expression in the mouse cortex after traumatic brain injury (TBI). We also simultaneously detected the altered mRNA profile to further analyze the possible function of lncRNA. Method C57BL/6 mice (n = 18) were used to construct a controlled cortical impact model. At 24 h post-TBI, the cortex around injury site was collected and the total RNA was extracted to construct the cDNA library. RNA sequencing (RNA-seq) was carried out followed by RT-PCR for confirmation. Bioinformatic analysis (including GO analysis, KEGG pathway and co-expression analysis) also were performed. Results A total of 64,530 transcripts were detected in the current sequencing study, in which 27,457 transcripts were identified as mRNA and 37,073 transcripts as lncRNA. A total of 1,580 mRNAs (1430 up-regulated and 150 down-regulated) and 823 lncRNAs (667 up-regulated and 156 down-regulated) were significantly changed according to the criteria (| log2(fold change) | >1 and P < 0.05). These altered mRNAs were mainly related to inflammatory and immunological activity, metabolism, neuronal and vascular network. The expression of single lncRNA may be related with several mRNAs, and so was the mRNA. Also, a total of 360 new mRNAs and 8,041 new lncRNAs were identified. The good reproducibility and reliability of RNA-seq were confirmed by RT-PCR. Conclusion Numerous lncRNAs and mRNAs were significantly altered in mouse cortex around the injury site 24 h after TBI. Our present data may provide a promising approach for further study about TBI.