Journal of Shandong University (Health Sciences) ›› 2023, Vol. 61 ›› Issue (11): 27-37.doi: 10.6040/j.issn.1671-7554.0.2023.0291

• Preclinical Medicine • Previous Articles    

Structural variation and expression analysis of mRNAome and lncRNAome in cortex of rat Middle Cerebral Artery Occlusion model

YUAN Shan, YANG Yuying, XU Meimei, HU Guangze, TANG Juan, GAO Rui   

  1. Department of Biochemistry, School of Medicine, Shihezi University /The Key Laboratory of Ministry of Education for Xinjiang Endemic &
    Ethnic Disease, Shihezi 832000, Xinjiang, China
  • Published:2023-12-12

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Abstract: Objective To explore the basic characteristics and expression patterns of mRNA transcriptome(mRNAome)and lncRNA transcriptome(lncRNAome)in the cortex tissue of middle cerebral artery occlusion(MCAO)rats by using deep sequencing technology, so as to provide available target genes and molecular markers for ischemic stroke. Methods After the hypoxic-ischemia and reperfusion injury model of MCAO rat model was established with thread embolism method, the availability was estimated with behavioral scoring and TTC staining. The full transcriptome of 10 cortical samples from the MCAO and sham groups were sequenced with deep sequencing technology. The mRNAome, lncRNAome, and their structural variations were identified with bioinformatics methods. The differentially expressed genes(DEGs)were verified with qRT-PCR. Results The MCAO model was successfully established. The brain tissue in the ischemic and hypoxic area showed pale after TTC staining, which was in sharp contrast to the ruddy color of the non-infarcted area. A total of 108.54 G clean sequencing data were obtained from high-throughput sequencing, and 30,829 and 311,183 mRNA and lncRNA transcripts were identified respectively. The total numbers of SNP and Indel produced by the MCAO group were significantly fewer than those by the sham group. However, there was no significant difference in the number of mRNA Indel between the two groups. The number of variants of mRNAome was significantly greater than that of lncRNAome, but there was no significant difference in the total number of variants of transcripts between the two groups. A total of 2,608 differentially expressed mRNA and 551 differentially expressed lncRNA were screened out. Altogether 9 known genes responding to ischemia and hypoxia were identified as the double-blind testers, which were verified in the up-regulated gene dataset in the MCAO group. The qRT-PCR results further confirmed that the expression trends of the 9 genes were the same as the sequencing data, indicating that the sequencing data were reliable. Conclusion A part of mRNA and lncRNA affecting the processing and splicing of transcripts are activated after hypoxic-ischemic and reperfusion injury, which may inhibit the transcription of some transcripts and the ability of RNA editing and processing, and then affect the expression of key target genes in ischemic stroke.

Key words: Middle cerebral artery occlusion, mRNA, lncRNA, Structure variation, Alternative splicing

CLC Number: 

  • R743
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