Identification of functional lncRNAs in pseudorabies virus type II infected cells

Long noncoding RNAs (lncRNAs) play important roles in the antiviral responses. However, little is known about the identification and functions of swine lncRNAs in response to pseudorabies virus type II (PRV-II). Here, we detected the expression profiles of host lncRNAs from a wild-type (PRV-II DX) and gE/TK deficient (gE-TK-PRV) PRV-II infected cells. RNA-seq identified 664 differentially expressed (DE) lncRNAs from PRV-DX infected cells, 654 DE lncRNAs from gE-TK-PRV infected cells and 276 DE lncRNAs between PRV-DX and gE-TK-PRV infected cells. The potential functions of the significant differentially expressed (SDE) lncRNAs were involved in interleukin secretion, axon extension and metabolic process based on the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, the expression patterns of sixteen SDE lncRNAs determined by RT-qPCR exhibited high correlation (r > 0.95) with those by RNA-seq results. Western blotting assay displayed the lncA02830 did not code for protein, and the silencing of lncA02830 could significantly up-regulate the transcription levels of IRF3, IFNβ as well as MX1 and inhibit the replication of PRV-II. Taken together, these data highlighted the potentials of lncRNA as targets for antiviral therapy and provided some novel knowledge of the mechanisms underlying the host interaction with PRV-II.