Transcriptome analysis of the mRNAs and lncRNAs in porcine alveolar macrophages in response to porcine reproductive and respiratory syndrome virus or IFN-a at different time points

Purpose:We performed next-generation RNA sequencing and a comprehensive bioinformatics analyses to characterize the transcriptome landscapes, including mRNAs and long noncoding RNAs (lncRNAs) in PRRSV-infected PAMs or IFN-stimulated PAMs at different time points. Conclusions: We showed that PRRSV infection displays different transcriptome profiles of PAMs, and the aberrant function of PAMs may be reflected by significant down-regulation of essential genes at the transcriptome levels. In addition, we discovered a great amount of differentially expressed lncRNAs, including lncRNA XR_297549.1, which is highly expressed and predicted to both cis- and trans-regulate its neighboring gene PTGS2.In addition, In order to expand our understanding of these IFN-induced non-coding transcripts, especially long non-coding RNAs (lncRNAs), we performed next-generation RNA sequencing and a comprehensive bioinformatics analysis of porcine alveolar macrophages (PAMs) stimulated with pig-IFN-? for 6h and 12h, respectively. A great amount of differentially expressed mRNAs and lncRNAs were identified, and several lncRNAs are of great interest for further investigation as their potential role in regulation of the well-characterized antiviral genes, such as OAS1, PML and ISG15. Examination of the differential expression profiles of primary porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus or stimulated with IFN-a with two biological replicates, using Illumina Higseq 2500.