Transcriptome Analysis Of Mouse Cells Infected With Vesicular Stomatitis Virus

Vesicular stomatitis virus(VSV)is a typical negative-strand RNA virus in the Rhabdoviridae family.It is often used as a model in biological research due to its easy culturing and mild symptoms of infection in humans.Previous studies have shown that after VSV infection in host cells,the matrix protein of the virus can interfere with nuclear-cytoplasmic transport of the nacent mRNAs in the host cell and prevent the mRNA from nuclear export.In order to comprehensively explore various changes of mRNA post-transcriptional processing in host cells after VSV infection and the effects of such changes on subcellular localization of mRNAs,we designed the cell fractionation experiment after VSV infection in mouse cells,and analyzed the RNA-seq data systematically.We firstly identified differentially expressed genes,and genes that undergo alternative splicing and alternative polyadenylation after VSV infection,and then performed gene set enrichment analysis to explore their biological functions and pathways.Furthermore,we analyzed the nucleoplasmic and cytoplasmic RNAs of mouse cells after VSV infection,and compared the differences in mRNA processing between the two cellular components.We found that intron retention events or 3 ’ UTR-shortened mRNAs tend to be enriched in the nucleoplasmic components in the later stages of infection,indicating that post-transcriptional processing of mRNA has an impact on its cellular localization.These results show the global transcriptome changes in mouse cells after VSV infection and the biological processes and pathways in which VSV may involve.This study provides rich data and theoretical basis for further research on the regulatory mechanism of RNA subcellular localization.