Global 3’-UTR Length Changes Form a Novel Layer of Regulation in the Macrophage Response to Interferon-Beta

Abstract

Interferon signaling is one of the most important mechanisms shaping innate immune responses and needs to be tightly regulated to successfully fight infections and modulate immune responses while avoiding toxicity. <br /> Type I interferons (IFNs) have been shown to induce multiple transcriptional, translational and metabolic changes. The global response of murine and human macrophages to IFNb stimulation was characterized in this study using multi- omics strategies. These analyses gave insight into a complex regulatory network of transcripts, proteins and metabolites that results in global reprogramming of the cell. <br /> Post-transcriptional gene regulation is an important component of this network and is centered around 3’-untranslated regions (3’-UTRs), regions heavily targeted by miRNAs and harboring binding sites for many RNA-binding proteins. Poly-A-tail sequencing (PAT-seq) experiments revealed that many transcripts expressed shortened 3’-UTRs in response to IFNb, a result of changed alternative polyadenylation (APA) patterns. <br /> APA and changed 3’-UTR lengths are emerging fields of broad importance in physiological and pathological processes that are only starting to be explored. Differences in APA patterns and their regulation have not previously been studied in context of IFN. <br /> Recent publications have described a scaffold-like role for 3’-UTRs that facilitates the formation of different protein complexes depending on 3’-UTR length, which can affect localization and function. This unique regulatory mechanism was investigated for two IFNß-regulated transcripts with shortened 3’-UTRs, EIF4EBP2 and MAVS. 3’-UTR-dependent protein-protein interactions were identified by mass spectrometry using tagged overexpression constructs encoding the different transcript isoforms. <br /> This study describes a new aspect of IFN signaling and a novel layer of regulation through genes that are not part of the typical and well-characterized IFN transcriptional response. It shows how differential expression of distinct 3’-UTR transcript isoforms influences macrophage innate immune responses.