The innate immune response of an organism is the primary response to challenges including inflammatory stimuli, infectious agents or the presence of cancer cells. The protective IFN activation and signalling is a key component of this response. IFN signalling is essential for host survival, fundamental to vaccine responses, can be activated therapeutically and is often the target for pathogen evasion strategies. While there is considerable knowledge of transcriptional regulation and role of protein coding transcripts in the IFN response equivalent knowledge of non-coding responses and their regulatory mechanism remain to be elucidated. Furthermore the role of miRNA in regulating the biological response to IFN remains limited.
The recently developed HITS-CLIP sequencing approach provides the ability to capture genome wide microRNA binding regulatory events. This approach provides a comprehensive measure of both microRNA and target UTR sequences through argonaut dependent RNA immunoprecipiation coupled with high throughput next generation sequencing. This study combines HITS-CLIP sequencing with traditional small and ribosomal depleted total RNA sequencing to provide a comprehensive understanding of the IFNβ response in macrophages. Computational analysis has identified 119 IFN regulated microRNA including 55 novel microRNA involved in 3865 regulatory interactions. Analysis and experimental validation of these networks has identified critical microRNA mediated regulatory modules. These include modules involved in homeostatic suppression of the primary IFN response, amplification of the signalling response through targeting of Socs1 and enhanced regulation of newly identified IFN suppressed genes. Integration of RNA sequencing data provides evidence of 3'UTR switching in target transcripts also forming an important component of this response.
This systems level interpretation of IFN mediated signaling has the potential to provide a basis for novel insights into both host-pathogen interactions and host response critical in the efficient development of effectively targeted therapeutics