RIG-I Recognizes the 5′ Region of Dengue and Zika Virus Genomes

Abstract

The flavivirus genus comprises major human pathogens, such as Dengue (DENV) and Zika (ZIKV) viruses. RIG-I and MDA5 are key cytoplasmic pathogen recognition receptors that are implicated in detecting viral RNAs. Here, we show that RNAs that co-purified with RIG-I during DENV infection are immuno-stimulatory, whereas RNAs bound to MDA5 are not. An affinity purification method combined with next-generation sequencing (NGS) revealed that the 5' region of the DENV genome is recognized by RIG-I. No DENV RNA was bound to MDA5. In vitro production of fragments of the DENV genome confirmed the NGS data and revealed that the 5' end of the genome, when bearing 5'-triphosphates, is the RIG-I ligand. The 5' region of the ZIKV genome is also a RIG-I agonist. We propose that RIG-I binds to the highly structured and conserved 5' region of flavivirus nascent transcripts before capping and that this mechanism leads to interferon secretion by infected cells.

Comparative Transcriptomic Analysis of Immune-Related Gene Expression in Duck Embryo Fibroblasts Following Duck Tembusu Virus Infection

“…As previously reported, MDA5 and RIG-I can recognize long RNA fragments or dsRNAs (not triphosphorylated) and 5′-triphosphorylated or short RNA fragments, respectively [5,34]. The two PRRs were also recognized by other flaviviruses, such as Dengue virus [35,36], Zika virus [34,37], Hepatitis virus [38], Japanese encephalitis virus [35,39], West nile virus [40,41], and Avian tembusu virus [5], indicating that DTMUV may trigger the same innate immune signaling pathway as the above flaviviruses. In this study, DTMUV was sensed by PRRs in DEFs, and various immune molecules were efficiently induced.…”

Y-RNAs Lead an Endogenous Program of RIG-I Agonism Mobilized upon RNA Virus Infection and Targeted by HIV

“…S1B). We previously reported specific viral RNA-binding profiles on RLR compared to non-specific binding (Cherry) upon MV and DV-4 infections ( 15, 16 ) (Fig. S1C-D).…”

“…In this work, we specifically identified the repeat family of Y-RNAs, and in particular RNY4, as a model of endogenous RNAs whose unique structure confers a previously unknown function as RIG-I agonists. We observed a contribution of Y-RNAs in RLR signaling during infections by MV and DV-4, both RNA viruses replicating in the cytoplasm and producing RLR-specific viral RNA ligands ( 15, 16 ). MV and DV-4 are acute viral infections where the speed of host response is critical to halt and ultimately clear viral replication.…”

“…We recently developed a riboproteomic approach based on tagged protein affinity purification that measures and compares receptor affinity of RNA molecules with improved statistical evaluation of specific binding ( 15, 16 ). We performed an unbiased quantification of RLR-bound self RNAs during RNA virus infection.…”

The Interplay between Dengue Virus and the Human Innate Immune System: A Game of Hide and Seek

“…This observation was then recapitulated in various cell types (Huh7 hepatocarcinoma cells, endothelial cells, and primary monocytes) and experimental settings [17,[40][41][42]. Combining affinity purification and next-generation sequencing, Chazal and colleagues recently showed that RIG-I is able to recognize 5 -ppp uncapped DENV vRNA, suggesting that detection of DENV nucleic acids occurs before the 5 -end maturation by capping is completed and that vRNA is afterwards hidden from PRR [43]. In stark contrast, the putative role of MDA5 in the detection of DENV nucleic acids remains unclear.…”