Double-stranded RNA triggers a distinct integrated stress response in the early embryo [RNA-seq, Ribo-seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE265771 | GEO | 2024/04/26
REPOSITORIES: GEO
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Project description:Gene functional study and the emerging mRNA therapy technology heavily rely on in vitro transcribed (IVT) mRNA, but the double-stranded RNA (dsRNA) by-product generated during IVT is often recognized by cells as a marker of virus replication, leading to the integrated stress response (ISR).The biological effects of dsRNA in undifferentiated cells differ significantly from those of differentiated counterparts.Here, we found that dsRNA triggered an unprecedented ISR in zebrafish early embryos, leading to developmental delay, severe cell necrosis, and lethal malformations.Mechanistically, dsRNA stimulation caused a PKR-eIF2α independent global translation inhibition and a burst of p53 signaling. In turn, p53 activated Interferon Stimulated Genes (ISGs) and other defense-related genes in the absence of the IFN system. Unexpectedly, p53 does not promote cell death; instead, it plays a protective role in weakening the damage of translation repression by compromising protein turnover via enhanced ISGylation.This study thus unveils a distinct ISR upon dsRNA stimulation, which may help perform faithful gene overexpression in early embryos and shed light on the strategies of undifferentiated cells against RNA virus infection.
2024-01-01 | GSE234229 | GEO
Project description:Gene functional study and the emerging mRNA therapy technology heavily rely on in vitro transcribed (IVT) mRNA, but the double-stranded RNA (dsRNA) by-product generated during IVT is often recognized by cells as a marker of virus replication, leading to the integrated stress response (ISR).The biological effects of dsRNA in undifferentiated cells differ significantly from those of differentiated counterparts.Here, we found that dsRNA triggered an unprecedented ISR in zebrafish early embryos, leading to developmental delay, severe cell necrosis, and lethal malformations.Mechanistically, dsRNA stimulation caused a PKR-eIF2α independent global translation inhibition and a burst of p53 signaling. In turn, p53 activated Interferon Stimulated Genes (ISGs) and other defense-related genes in the absence of the IFN system. Unexpectedly, p53 does not promote cell death; instead, it plays a protective role in weakening the damage of translation repression by compromising protein turnover via enhanced ISGylation.This study thus unveils a distinct ISR upon dsRNA stimulation, which may help perform faithful gene overexpression in early embryos and shed light on the strategies of undifferentiated cells against RNA virus infection.
2024-01-01 | GSE234227 | GEO
Project description:During infection, interferon production leads to upregulation of the interferon-stimulated gene 15 (ISG15) which encodes the ubiquitin-like protein ISG15. ISG15 has a profound role in restricting intracellular infection by viral and bacterial pathogens. It can exert its function either as a free intracellular or extracellular molecule, or as an ubiquitin-like conjugate to substrate proteins in a process called ISGylation. Here, we used a viral-like particle trapping (Virotrap) technology and GST pull down, both coupled to mass spectrometry, to screen for intracellular ISG15-binding proteins. As strongest hit, we identified RNF213, a very large interferon-induced protein targeted to lipid droplets and a genetic risk factor for Moyamoya disease, a rare cerebrovascular disorder. We verified binding of ISG15 and RNF213 with biochemical methods and imaging and found that interferon signaling induces ISGylation and oligomerization of RNF213 on the surface of lipid droplets, acting as a binding platform for ISGylated proteins. Moreover, we showed that knockdown of RNF213 promotes in vitro infection by Listeria monocytogenes, respiratory syncytial virus (RSV) and Coxsackie virus (CV) B3, suggesting a broad antimicrobial activity of RNF213. In contrast, overexpression of RNF213 restricted Listeria infection and was associated with a striking co-localization of RNF213 with intracellular bacteria. Infection experiments in RNF213 deficient mice corroborated these results in vivo, revealing a so far unknown function of RNF213 in the host defense against infection. Together, we report that RNF213 assembles into a binding platform for ISGylated proteins on the surface of lipid droplets, acting as a first step of an antimicrobial cellular pathway that processes ISGylated proteins. Our findings provide novel molecular insights into the ISGylation pathway and point towards an important role of the immune response to infection in the etiology of Moyamoya disease.
2021-08-16 | PXD018346 | Pride
Project description:During infection, interferon production leads to upregulation of the interferon-stimulated gene 15 (ISG15) which encodes the ubiquitin-like protein ISG15. ISG15 has a profound role in restricting intracellular infection by viral and bacterial pathogens. It can exert its function either as a free intracellular or extracellular molecule, or as an ubiquitin-like conjugate to substrate proteins in a process called ISGylation. Here, we used a viral-like particle trapping (Virotrap) technology and GST pull down, both coupled to mass spectrometry, to screen for intracellular ISG15-binding proteins. As strongest hit, we identified RNF213, a very large interferon-induced protein targeted to lipid droplets and a genetic risk factor for Moyamoya disease, a rare cerebrovascular disorder. We verified binding of ISG15 and RNF213 with biochemical methods and imaging and found that interferon signaling induces ISGylation and oligomerization of RNF213 on the surface of lipid droplets, acting as a binding platform for ISGylated proteins. Moreover, we showed that knockdown of RNF213 promotes in vitro infection by Listeria monocytogenes, respiratory syncytial virus (RSV) and Coxsackie virus (CV) B3, suggesting a broad antimicrobial activity of RNF213. In contrast, overexpression of RNF213 restricted Listeria infection and was associated with a striking co-localization of RNF213 with intracellular bacteria. Infection experiments in RNF213 deficient mice corroborated these results in vivo, revealing a so far unknown function of RNF213 in the host defense against infection. Together, we report that RNF213 assembles into a binding platform for ISGylated proteins on the surface of lipid droplets, acting as a first step of an antimicrobial cellular pathway that processes ISGylated proteins. Our findings provide novel molecular insights into the ISGylation pathway and point towards an important role of the immune response to infection in the etiology of Moyamoya disease.
2021-08-16 | PXD018345 | Pride
Project description:Interferon (IFN)-stimulated gene 15 (ISG15), a ubiquitin-like protein, is covalently conjugated to host immune proteins such as MDA5 and IRF3 in a process called ISGylation, thereby promoting type I interferon (IFN) induction to limit the replication of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, whether SARS-CoV-2 proteins can be directly targeted for ISGylation remains elusive. In this study, we identified the nucleocapsid (N) protein of SARS-CoV-2 as a major substrate of ISGylation catalyzed by the host E3 ligase HERC5; however, N ISGylation is readily removed through de-ISGylation by the papain-like protease (PLpro) activity of NSP3. Mass spectrometry analysis identified that the N protein undergoes ISGylation at four lysine residues (K266, K355, K387 and K388), and mutational analysis of these sites in the context of a SARS-CoV-2 replicon (N-4KR) abolished N ISGylation and alleviated ISGylation-mediated inhibition of viral RNA synthesis. Furthermore, our results indicated that HERC5 targets preferentially phosphorylated N protein for ISGylation to regulate its oligomeric assembly. These findings reveal a novel mechanism by which the host ISGylation machinery directly targets SARS-CoV-2 proteins to restrict viral replication and illuminate how an intricate interplay of host (HERC5) and viral (PLpro) enzymes coordinates viral protein ISGylation and thereby regulates virus replication.
2024-08-14 | PXD053712 | Pride
Project description:Loss of RNA homeostasis underlies numerous neurodegenerative and neuroinflammatory diseases. However, the molecular mechanisms that trigger neuroinflammation are poorly understood. Viral double-stranded RNA (dsRNA) triggers innate immune responses when sensed by host pattern recognition receptors (PRRs) present in all cell types. Here, we report that human neurons intrinsically carry exceptionally high levels of immunostimulatory dsRNAs and identify long 3'UTRs as giving rise to neuronal dsRNA structures. We found that the neuron-enriched ELAVL family of genes (ELAVL2, -3, -4) can increase 1) 3'UTR length, 2) dsRNA load, and 3) activation of dsRNA-sensing PRRs such as MDA5, PKR, and TLR3. In wild-type neurons, neuronal dsRNAs signaled through PRRs to induce tonic production of the antiviral type I interferon. Depleting ELAVL2 in WT neurons led to global shortening of 3'UTR length, reduced immunostimulatory dsRNA levels, and rendered WT neurons susceptible to herpes simplex virus and Zika virus infection. Neurons deficient in ADAR1, a dsRNA-editing enzyme mutated in the neuroinflammatory disorder Aicardi-Goutières syndrome, exhibited intolerably high levels of dsRNA that triggered PRR mediated toxic inflammation and neuronal death. Depleting ELAVL2 in ADAR1 knockout neurons led to prolonged neuron survival by reducing immunostimulatory dsRNA levels. In summary, neurons are specialized cells where PRRs constantly sense ‘self’ dsRNAs to pre-emptively induce protective antiviral immunity, but maintaining RNA homeostasis is paramount to prevent pathological neuroinflammation.
2023-10-20 | GSE214949 | GEO
Project description:Double-stranded RNA (dsRNA) can enter different pathways in mammalian cells, such as the sequence-specific RNA interference (RNAi) pathway, the sequence-independent interferon response, and RNA editing by adenosine deaminases. To study routing of long dsRNA into different pathways in different tissues, we generated transgenic mice carrying an inverted repeat transcribed by a strong, ubiquitously active polII promoter. Here, we provide the first report of effects caused by ubiquitous long dsRNA expression in the adult mouse. Long dsRNA is poorly processed into siRNAs in somatic cells but readily induces the RNAi effects in the oocyte, suggesting that somatic cells are missing a component of RNAi that facilitates siRNA biogenesis. Expression of dsRNA is not sufficient to activate the interferon pathway and has a minimal effect on the transcriptome in somatic cells. The interferon response in somatic cells could be induced with high doses of dsRNA expression, suggesting that somatic cells can tolerate endogenous dsRNA expression to a large extent. Our data demonstrate that the association between long dsRNA and the interferon pathway in somatic cells cannot be generalized and that cells recognize other features of dsRNA molecules, which increase or reduce the likelihood activation of a particular dsRNA-induced pathway. Brain or kidney tissue (transgenic mice), or HEK293 or HeLa cell lines (human), expressing long dsRNA within the 3'-UTR of the EGFP reporter gene.
2011-10-10 | E-GEOD-26577 | biostudies-arrayexpress
Project description:In mammals, double-stranded RNA (dsRNA) plays roles in sequence-specific RNA interference, sequence-independent interferon response, and RNA editing by adenosine deaminases. We have previously shown that long hairpin dsRNA expression in cultured cells does not activate the interferon response, it is poorly processed into siRNAs, and it is partially edited. Here, we demonstrate that dsRNA expressed from transiently transfected plasmids strongly inhibits expression of co-transfected reporter plasmids but not expression of endogenous genes or reporters stably integrated in the genome. The inhibition is concentration-dependent and independent of a cell type, transfection method, or dsRNA sequence. The inhibition occurs at the level of translation and is mediated by protein kinase R (PKR). PKR binds the expressed dsRNA, becomes phosphorylated and changes its distribution along polysome fractions. In conclusion, we demonstrate that expression from plasmids is selectively repressed if one of co transfected plasmids produces dsRNA. Our results highlight the importance of proper controls and careful interpretation of co-transfection experiments. HEK293 cells (human origin) were transiently transfected with hairpin dsRNA-expressing (MosIR) and control (pCag) plasmids.
2013-12-27 | E-GEOD-46959 | biostudies-arrayexpress
Project description:The function and mechanism of the interferon-regulated antiviral responses have been extensively characterized. Recent studies have demonstrated induction of antiviral RNA interference (RNAi) in somatic cells against several mammalian RNA viruses rendered incapable of RNAi suppression. However, little is known about Dicer-mediated production of virus-derived small-interfering RNAs (vsiRNAs) in these cells active in the type I interferon response. Here we show that the dsRNA precursors of influenza vsiRNAs were processed more efficiently than cellular precursor microRNA hairpins by wild-type human Dicer expressed de novo in Dicer-knockout somatic cells. We found that infection of two strains of suckling mice with wild-type Nodamura virus (NoV) was associated with production of silencing-active vsiRNAs and direct sequestration of duplex vsiRNAs by its RNAi suppressor protein B2. Our findings from in vivo infection with Sindbis virus recombinants expressing NoV B2 or carrying a vsiRNA-targeted insert provide evidence for an antiviral function of the induced RNAi response. Interestingly, NoV infection induces expression of RIG-I-like receptor LGP2 to inhibit vsiRNA biogenesis and promote virulent infection in suckling mice. Our findings together reveal efficient Dicer processing of vsiRNA precursors in interferon-competent somatic cells and suckling mice in contrast to synthetic long dsRNA examined previously by in vitro dicing.
2021-07-28 | GSE155146 | GEO
Project description:Double-stranded RNA (dsRNA) can enter different pathways in mammalian cells, such as the sequence-specific RNA interference (RNAi) pathway, the sequence-independent interferon response, and RNA editing by adenosine deaminases. To study routing of long dsRNA into different pathways in different tissues, we generated transgenic mice carrying an inverted repeat transcribed by a strong, ubiquitously active polII promoter. Here, we provide the first report of effects caused by ubiquitous long dsRNA expression in the adult mouse. Long dsRNA is poorly processed into siRNAs in somatic cells but readily induces the RNAi effects in the oocyte, suggesting that somatic cells are missing a component of RNAi that facilitates siRNA biogenesis. Expression of dsRNA is not sufficient to activate the interferon pathway and has a minimal effect on the transcriptome in somatic cells. The interferon response in somatic cells could be induced with high doses of dsRNA expression, suggesting that somatic cells can tolerate endogenous dsRNA expression to a large extent. Our data demonstrate that the association between long dsRNA and the interferon pathway in somatic cells cannot be generalized and that cells recognize other features of dsRNA molecules, which increase or reduce the likelihood activation of a particular dsRNA-induced pathway.
2011-10-11 | GSE26577 | GEO