A novel intronic circular RNA antagonizes influenza virus by absorbing a miRNA that degrades CREBBP and accelerating IFN-β production

Virus-host interactions are complicated processes, and multiple cellular proteins have been reported to promote or inhibit viral replication through different mechanisms. Recent progress has implicated circular RNAs (circRNA) in cancer biology and progression; however, the role of circRNAs in viral infection remains largely unclear. Here, we detected 11,620 circRNAs in A549 cells and found that 411 of them were differentially expressed in influenza virus-infected A549 cells. We characterized a novel intronic circRNA, AIVR, that was upregulated in influenza virus-infected A549 cells, and found that silencing of AIVR significantly promoted influenza virus replication in A549 cells. We further found that AIVR predominantly localizes in the cytoplasm and works as a microRNA (miRNA) sponge. One of the miRNAs absorbed by AIVR binds the mRNA of CREBBP, which is an important component of the large nucleoprotein complex IFN-β enhanceosome that accelerates IFN-β production. AIVR-overexpression significantly increased the mRNA and protein levels of INF-β in the influenza virus-infected A549 cells. Therefore, the upregulation of AIVR is a cellular antiviral strategy, with AIVR exerting its antiviral effect by absorbing miRNA and promoting the expression of CREBBP to facilitate IFN-β production. Our study provides new insights into the roles of circRNAs in the cellular innate antiviral response. To investigate the differential expression of circRNAs in influenza virus-infected cells, human alveolar epithelial cells (A549) were mock-infected or infected with an H9N2 avian influenza virus, A/chicken/Jiangsu/C4258/12 (H9N2) (H9N2 virus). At 12 h post-infection (p.i.), total RNA was extracted from the cells, and the circRNAs, miRNAs, and mRNAs were deep-sequenced and computationally analyzed.