Global biochemical analysis reveals miRNA-RNA virus and miRNA-enhancer targets regulating immune signalling in Respiratory syncytial virus infection

Abstract microRNAs (miRNAs) regulate nearly every physiological process but our understanding of exactly how they function remains incomplete, particularly in the context of viral infection. Target prediction models are built on canonical miRNA interactions with 3’untranslated regions (3’UTRs) and post-transcriptional gene suppression, leaving a gap in knowledge on other types of targets and capacity for direct interactions with viral genomes. Here we adapt a biochemical method to globally identify targets of human miRNAs in lung cells including scope for direct interactions with Respiratory syncytial virus (RSV). We show that RSV binds miR-26, miR-27, and let-7, leading to de-repression of miRNA targets associated with cell cycle regulation and immune signalling. Using our bioinformatics pipeline to determine high confidence targets in the human genome we further discover that pseudogenes which overlap transcriptional regulatory regions are functional miRNA targets. We identify and validate an interaction between miR-27 and a pseudogene-derived lncRNA that regulates transcription of Carcinoembryonic antigen-related cell adhesion molecule 1 ( CEACAM1 ). This work demonstrates that RSV directly interacts with host miRNAs to de-regulate host gene expression and provides biochemical support for the ability of miRNAs to directly regulate gene transcription linked to immune signalling.