The contribution of pre-mRNA processing mechanisms to the regulation of immune responses remains poorly studied despite emerging examples of their role as regulators of immune defenses. We sought to investigate the role of mRNA processing in the cellular responses of human macrophages to live bacterial infections. Here, we used mRNA sequencing to quantify gene expression and isoform abundances in primary macrophages from 60 individuals, before and after infection with Listeria monocytogenes and Salmonella typhimurium . In response to both bacteria we identified thousands of genes that significantly change isoform usage in response to infection, characterized by an overall increase in isoform diversity after infection. In response to both bacteria, we found global shifts towards ( i ) the inclusion of cassette exons and ( ii ) shorter 3’ UTRs, with near-universal shifts towards usage of more upstream polyadenylation sites. Using complementary data collected in non-human primates, we show that these features are evolutionarily conserved among primates. Following infection, we identify candidate RNA processing factors whose expression is associated with individual-specific variation in isoform abundance. Finally, by profiling microRNA levels, we show that 3’ UTRs with reduced abundance after infection are significantly enriched for target sites for particular miRNAs. These results suggest that the pervasive usage of shorter 3’ UTRs is a mechanism for particular genes to evade repression by immune-activated miRNAs. Collectively, our results suggest that dynamic changes in RNA processing may play key roles in the regulation of innate immune responses. Author Summary Changes in gene regulation have long been known to play important roles in both innate and adaptive immune responses. While transcriptional responses to infection have been well-characterized, much less is known about the extent to which co-transcriptional mechanisms of mRNA processing are involved in the regulation of immune defenses. In this study, we sought to investigate the role of mRNA processing in the cellular responses of human macrophages to live bacterial infection. Using primary human macrophages derived from whole blood samples from 60 individuals, we sequenced mRNA both before and after infection with two live bacteria. We show that immune responses to infection are accompanied by pervasive changes in mRNA isoform usage, with systematic shifts towards increased cassette exon inclusion and shortening of Tandem 3’ UTRs post-infection. These patterns are conserved in nonhuman primates, supporting their functional importance across evolutionary time. Complementary microRNA profiling revealed that shortened 3’ UTRs are enriched for target sites of macrophage-expressed miRNAs, many of which are specifically activated after infection to regulate the innate immune response. Our results therefore provide the first genome-wide empirical support for the idea that actively regulated shifts towards shorter 3’ UTRs might allow specific genes to evade repression by immune-activated miRNAs.
【초록키워드】 Macrophage, immune response, Gene Expression, innate immune response, macrophages, Variation, Sequencing, microRNA, Infection, immune, RNA, miRNAs, non-human primates, mRNA, immune responses, Bacterial infection, Gene regulation, Bacteria, repression, human macrophage, expression, change, Bacterial infections, mechanism, cellular response, Listeria monocytogenes, regulate, adaptive immune responses, complementary, Cellular responses, Salmonella Typhimurium, Support, Post-infection, Factor, Regulation, Usage, idea, ExoN, transcriptional response, primates, innate immune responses, polyadenylation sites, UTRs, upstream, human macrophages, shortening, transcriptional responses, while, tandem, isoform, Inclusion, feature, whole blood sample, identify, collected, sequenced, conserved, example, significantly, involved, reduced, characterized, functional, activated, less, changes in, increase in, regulated, evade, individuals, accompanied, 3’ UTR, Listeria monocytogene, pre-mRNA, 【제목키워드】 Region, immune responses, response, Innate, ExoN, Increased,