Altered expressions of long non-coding RNA and mRNA in mouse cortex after subarachnoid hemorrhage

Abstract

Objective To investigate the differential expressions of long non-coding RNAs (lncRNAs) and mRNAs in early phases of subarachnoid hemorrhage (SAH) and explore the possible new mechanisms which may regulate early brain injury (EBI). Methods A total of 6 C57BL/6J male wild-type mice were divided into sham-operated group and SAH group (n=3). SAH models were induced by endovascular perforation. Twenty-four hours after operation, all animals were sacrificed, brain samples were removed rapidly, and total RNAs were extracted. After quality control, total RNAs were amplified and transcribed into fluorescent cRNA, and then performed RNA-seq by an Illumina HiSeqTM2500. Reads were aligned to the mouse transcriptome with Tophat2 software. The whole sample expression levels were presented by RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions base pairs Sequenced). The differential expressions of mRNAs were analyzed by biological pathways, and all the differentially expressed mRNAs were selected for Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Quantitative real-time (qRT)-PCR was used to confirm some differentially expressed mRNAs. Results The expression profiles of lncRNAs and mRNAs of sham-operated and SAH mice brain tissues were successfully analyzed by RNA-Seq. In these 6 samples, 617 lncRNAs (103 being upregulated and 514 being downregulated) and 444 mRNAs (387 being upregulated and 54 being downregulated) were differentially expressed in three pair brain tissues. GO and KEGG analysis indicated that differentially expressed mRNAs were involved in a variety of biological processes, including inflammation. The qRT-PCR analysis of 4 randomly selected lncRNAs (fantom3_C730003K16 and fantom3_I830129C17 up-regulation expressions; fantom3_A430024L20 and fantom3_C330006P03 down-regulation expressions) confirmed the accuracy of RNA-seq. Conclusion LncRNAs significantly differentially express in the SAH brain tissues and the sham-operated brain tissues; LncRNA is a promising potential therapeutic target for the prognosis, diagnosis and treatment of SAH. Key words: Subarachnoid hemorrhage; Early brain injury; Long non-coding RNA; Inflammation; Next-generation sequencing