MicroRNA expression profiling in Newcastle disease virus-infected DF-1 cells by deep sequencing

Newcastle disease virus (NDV), causative agent of Newcastle disease (ND), is one of the most devastating pathogens for poultry industry worldwide. MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by regulating mRNA translation efficiency or mRNA abundance through binding to mRNA directly. Accumulating evidence has revealed that cellular miRNAs can also affect virus replication by controlling host-virus interaction. To identify miRNA expression profile and explore the roles of miRNA during NDV replication, in this study, small RNA deep sequencing were performed of non-inoculated DF-1 cells (chicken embryo fibroblast cell line) and JS 5/05-infected cells collected at 6h and 12 h post infection (hereafter called mock，NDV-6h and NDV-12 h group respectively). 73 miRNAs of NDV-6h group and 64miRNAs of NDV-12h group were significantly differentially expressed (SDE) when compared with those in mock group. Meanwhile, 50 SDE miRNAs, including 48 up- and 2 downregulated, showed the same expression patterns in NDV-6h and NDV-12h group. QRT-PCR validation of 15 selected miRNAs’ expression patterns were consistent with deep sequencing. To investigate the role of these SDE miRNAs in NDV replication, miRNA mimics and inhibitors were transfected into DF-1 cells followed by NDV infection. The results revealed that gga-miR-451 and gga-miR-199-5p promoted NDV replication while gga-miR-19b-3p and gga-miR-29a-3p inhibited NDV replication. Further function research demonstrated gga-miR-451 suppressed NDV-induced inflammatory response via targeting YWHAZ (tyrosine3-monooxygenase/tryptophan5-monooxygenase activation protein zeta). Overall, our study presented a global miRNA expression profile in DF-1 cells in response to NDV infection and verified the roles of some SDE miRNAs in NDV replication which will underpin further studies of miRNAs’ roles between the host and the virus.