GO:0039536 negative regulation of RIG-I signaling pathway: Immune Checkpoint, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0039536 describes any process that stops, prevents, or reduces the RIG-I signaling pathway, a key cytosolic antiviral RNA-sensing cascade.
• Negative regulators act at multiple nodes: RIG-I itself, MAVS, STING, and downstream interferon effectors.
• Key negative regulators include RNF125, SEC14L1, Tim-3, IRGM, and TRIM13, which promote ubiquitination, degradation, or sequestration of pathway components.
• Dysregulation of this checkpoint contributes to viral susceptibility, autoimmunity, and cancer immune evasion.
• CRISPR knockout, point mutation, knock-in, and overexpression models are essential to dissect causal roles of negative regulators.
• The pathway is conserved from fish to mammals, offering diverse model systems for functional studies.
Description
The RIG-I signaling pathway is a cornerstone of innate antiviral immunity, detecting cytosolic short double-stranded RNA and triggering interferon production. To prevent excessive or prolonged immune activation, cells deploy negative regulatory mechanisms collectively annotated as GO:0039536, negative regulation of RIG-I signaling pathway. This process is essential for balancing antiviral defense with immune homeostasis, and its perturbation is linked to viral pathogenesis and autoimmune disorders. Researchers study this term to identify checkpoints that can be therapeutically targeted in infections, autoimmunity, and cancer. The pathway is evolutionarily conserved, with negative regulators identified in fish and mammals, underscoring its fundamental importance. Understanding these mechanisms at molecular resolution requires precise genetic models and functional assays.
negative regulation of RIG-I signaling pathway At A Glance
| GO ID | GO:0039536 |
|---|---|
| GO term | negative regulation of RIG-I signaling pathway |
| Ontology | biological_process |
| Synonym | negative regulation of DDX58 signaling pathway; negative regulation of retinoic acid inducible gene I signaling pathway; negative regulation of RIG-I signalling pathway |
| Major function | Dampening cytosolic antiviral RNA sensing to prevent excessive interferon and inflammatory responses |
| Key regulators | RNF125, SEC14L1, Tim-3, IRGM, TRIM13, and others |
| Pathway nodes | RIG-I, MAVS, STING, TBK1, IRF3/7 |
| Conservation | Present in fish and mammals |
What Is GO:0039536?
GO:0039536 encompasses any biological process that stops, prevents, or reduces the frequency, rate, or extent of the RIG-I signaling pathway, also known as the DDX58 signaling pathway. This includes mechanisms that degrade or inhibit RIG-I, MAVS, or downstream adaptors, thereby dampening interferon and cytokine responses.
Why Is negative regulation of RIG-I signaling pathway Important in Cell Biology?
Negative regulation of RIG-I signaling is critical for preventing autoimmunity and inflammatory pathology while allowing effective antiviral defense. Its dysregulation is implicated in viral susceptibility, autoimmune diseases, and cancer immune evasion, making it a high-value target for therapeutic intervention.
• Prevents excessive interferon production that can cause autoinflammatory disease.
• Controls viral pathogenesis, as seen with Tim-3-mediated enhancement of H1N1 infection.
• Modulates cancer immunity through IRGM suppression of cGAS-STING and RIG-I-MAVS.
• Provides targets for antiviral therapy, e.g., blocking Tim-3 to reduce H1N1.
• Influences vaccine adjuvant design by tuning innate immune activation.
• Conserved in fish, offering comparative immunology insights.
• Involves ubiquitin ligases like RNF125 that are potential drug targets.
• Impacts STING trafficking and ER adaptor function.
• Regulates autophagy-mediated degradation of MAVS by TRIM13.
• SEC14L1 provides a negative feedback mechanism.
What Happens During negative regulation of RIG-I signaling pathway?
Recognition and Initiation of RIG-I Signaling
In simple terms: RIG-I detects viral RNA and starts an alarm.
RIG-I (DDX58) binds short double-stranded RNA with 5' triphosphate, undergoes conformational change, and interacts with MAVS on mitochondria, leading to TBK1/IRF3 activation and interferon production.
Ubiquitination and Degradation of RIG-I
In simple terms: Tagging RIG-I for destruction stops the alarm.
The ubiquitin ligase RNF125 conjugates ubiquitin to RIG-I, promoting its proteasomal degradation and thereby terminating signaling.
Inhibition by SEC14L1
In simple terms: SEC14L1 blocks RIG-I's ability to signal.
SEC14L1 negatively regulates RIG-I-mediated antiviral signaling, likely by interfering with RIG-I activation or its interaction with MAVS.
Tim-3-Mediated Suppression
In simple terms: Tim-3 acts as a brake on RIG-I to help viruses.
Tim-3 negatively regulates RIG-I, and its expression promotes H1N1 infection by dampening antiviral responses.
IRGM Suppression of RIG-I-MAVS and cGAS-STING
In simple terms: IRGM turns down multiple alarm pathways.
IRGM suppresses both cGAS-STING and RIG-I-MAVS signaling to control interferon responses, linking autophagy-related proteins to innate immune checkpoints.
TRIM13-Mediated Autophagic Degradation of MAVS
In simple terms: TRIM13 sends MAVS to the recycling bin.
Avian TRIM13 targets MAVS for autophagic degradation, attenuating antiviral innate immunity.
Key Genes Involved in GO:0039536 negative regulation of RIG-I signaling pathway
The following genes and proteins are central to the negative regulation of RIG-I signaling, as supported by published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| RNF125 | E3 ubiquitin ligase that ubiquitinates RIG-I for degradation | Target for modulating RIG-I stability |
| SEC14L1 | Negative regulator of RIG-I-mediated signaling | Potential antiviral target |
| HAVCR2 (Tim-3) | Inhibits RIG-I, promoting H1N1 infection | Immune checkpoint in viral infection |
| IRGM | Suppresses cGAS-STING and RIG-I-MAVS signaling | Autoimmunity and autophagy link |
| TRIM13 | Targets MAVS for autophagic degradation | Avian antiviral immunity |
| DDX58 (RIG-I) | Cytosolic RNA sensor initiating signaling | Core pathway component |
| MAVS | Mitochondrial adaptor for RIG-I signaling | Central node for negative regulation |
| STING1 | ER adaptor facilitating innate immune signaling | Cross-talk with RIG-I pathway |
| TBK1 | Kinase activating IRF3/7 | Downstream effector |
| IRF3 | Transcription factor for interferon genes | Readout of pathway activity |
| IRF7 | Transcription factor for interferon genes | Readout of pathway activity |
| NFKB1 | Transcription factor for inflammatory cytokines | Pathway crosstalk |
| ATG5 | Autophagy machinery component | Autophagic degradation of MAVS |
| ATG7 | Autophagy machinery component | Autophagic degradation of MAVS |
| MAP1LC3B | Autophagosome marker | Autophagy assays |
| SQSTM1 | Autophagy receptor | Selective autophagy |
| USP21 | Deubiquitinase (context-dependent) | Potential regulator |
| NLRX1 | Negative regulator of RIG-I signaling | Mitochondrial checkpoint |
How Is negative regulation of RIG-I signaling pathway Regulated?
Negative regulation of RIG-I signaling is itself tightly controlled. For example, IRGM suppresses both cGAS-STING and RIG-I-MAVS pathways to control interferon responses. Tim-3 expression is induced upon infection and acts as a negative feedback loop. Ubiquitination and autophagy are key post-translational mechanisms, with RNF125 and TRIM13 mediating degradation of RIG-I and MAVS, respectively. SEC14L1 provides an additional layer of inhibition.
negative regulation of RIG-I signaling pathway and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| HAVCR2 (Tim-3) | H1N1 influenza susceptibility | KO mice, overexpression cell lines |
| IRGM | Autoimmunity, cancer immune evasion | KO and knock-in models |
| RNF125 | Antiviral response regulation | KO cells, point mutants |
| SEC14L1 | Viral infection control | Overexpression and KO |
| TRIM13 | Avian antiviral immunity | Knock-in and KO in avian cells |
Viral Infections
Negative regulators such as Tim-3 can enhance viral replication by dampening RIG-I signaling, as shown for H1N1 influenza. Targeting these checkpoints may restore antiviral immunity.
Autoimmunity
IRGM suppresses cGAS-STING and RIG-I-MAVS to prevent excessive interferon, and its dysfunction is linked to autoimmune conditions. Loss of negative regulation can lead to autoinflammatory phenotypes.
Cancer
IRGM-mediated suppression of innate immune signaling may contribute to immune evasion in cancer, making it a potential target for immunotherapy.
From negative regulation of RIG-I signaling pathway-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does RNF125 negatively regulate RIG-I? | RNF125 KO cells with RIG-I reporter |
| How does Tim-3 inhibit RIG-I? | Tim-3 overexpression and KO in H1N1 infection |
| Does IRGM suppress RIG-I-MAVS? | IRGM KO and overexpression |
| Is SEC14L1 a negative regulator? | SEC14L1 KO and overexpression |
| Does TRIM13 target MAVS for autophagy? | TRIM13 KO with autophagy flux assays |
| Is the pathway conserved in fish? | Fish RLR KO models |
How to Study the negative regulation of RIG-I signaling pathway Process
| Method | What It Measures | Typical Application |
|---|---|---|
| CRISPR KO screen | Loss-of-function phenotypes | Identify negative regulators |
| RNA-seq | Gene expression changes | Interferon signature |
| Proteomics | Protein abundance and modifications | Ubiquitination of RIG-I |
| Co-IP | Protein-protein interactions | RIG-I-MAVS binding |
| Autophagy flux | LC3B turnover | MAVS degradation |
| Reporter assays | ISRE/IFN-beta promoter activity | Pathway activity |
| qPCR | Viral RNA and ISG mRNA | Infection assays |
| Flow cytometry | Surface Tim-3 expression | Immune checkpoint |
CRISPR Knockout Screening
Genome-wide CRISPR knockout screens can identify negative regulators of RIG-I signaling by selecting for cells with enhanced interferon responses upon viral infection.
RNA-seq and Transcriptomics
RNA-seq measures interferon-stimulated genes and inflammatory cytokines to quantify pathway activity after perturbation of candidate regulators.
Proteomics and Ubiquitinomics
Mass spectrometry-based proteomics can detect ubiquitination and degradation of RIG-I, MAVS, and STING, revealing post-translational regulation.
Imaging and Autophagy Flux
Fluorescence microscopy and autophagy flux assays (LC3B, SQSTM1) visualize MAVS degradation and autophagosome formation.
How CRISPR Can Be Used to Study GO:0039536 negative regulation of RIG-I signaling pathway
Knockout
CRISPR knockout of candidate negative regulators such as RNF125, SEC14L1, or IRGM can confirm their role in suppressing RIG-I signaling, leading to enhanced interferon responses.
Point Mutation
Point mutations in catalytic residues of RNF125 or in the RIG-I interaction domain of SEC14L1 can dissect domain-specific functions.
Knock-in
Knock-in of tagged versions (e.g., HA-RNF125) allows tracking of protein localization and interaction dynamics.
Overexpression
Overexpression of Tim-3 or TRIM13 can recapitulate negative regulation and viral susceptibility phenotypes.
How EDITGENE Supports negative regulation of RIG-I signaling pathway Research
Researchers studying negative regulation of RIG-I signaling pathway-related genes often need to determine whether a candidate gene is causally involved in dampening antiviral responses. EDITGENE provides comprehensive CRISPR services to accelerate this discovery.
Contact EDITGENE today to design your custom CRISPR model for negative regulation of RIG-I signaling pathway research.
Frequently Asked Questions About negative regulation of RIG-I signaling pathway
What is negative regulation of RIG-I signaling pathway?
It is any process that stops, prevents, or reduces the RIG-I signaling pathway, a key antiviral RNA-sensing cascade.
What genes are involved in negative regulation of RIG-I signaling pathway?
Key genes include RNF125, SEC14L1, HAVCR2 (Tim-3), IRGM, and TRIM13.
How does RNF125 negatively regulate RIG-I?
RNF125 ubiquitinates RIG-I, targeting it for proteasomal degradation.
What is the role of Tim-3 in RIG-I signaling?
Tim-3 negatively regulates RIG-I and promotes H1N1 infection.
How does IRGM suppress RIG-I signaling?
IRGM suppresses both cGAS-STING and RIG-I-MAVS signaling to control interferon responses.
Is negative regulation of RIG-I signaling conserved in fish?
Yes, negative regulation of RLR signaling has been described in fish.
What diseases are linked to dysregulation of this pathway?
Viral infections, autoimmunity, and cancer immune evasion.
What experimental models are used to study this pathway?
CRISPR knockout, knock-in, overexpression, and reporter assays.
How does SEC14L1 inhibit RIG-I signaling?
SEC14L1 negatively regulates RIG-I-mediated antiviral signaling.
What is the role of TRIM13 in this pathway?
TRIM13 targets MAVS for autophagic degradation, attenuating antiviral immunity.
Conclusion
Negative regulation of RIG-I signaling (GO:0039536) is a vital immune checkpoint that balances antiviral defense and immune homeostasis. Its dysregulation contributes to viral susceptibility, autoimmunity, and cancer, making it a compelling therapeutic target. CRISPR-based models and functional genomics are essential to dissect the underlying mechanisms and identify new drug targets.
References
- 1. Quicke KM et al.. 2017. Negative regulators of the RIG-I-like receptor signaling pathway.. Eur J Immunol 47(4):615-628 PMID: 28295214
- 2. Chang MX. 2021. The negative regulation of retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) signaling pathway in fish.. Dev Comp Immunol 119:104038 PMID: 33548290
- 3. Ishikawa H et al.. 2008. STING is an endoplasmic reticulum adaptor that facilitates innate immune signalling.. Nature 455(7213):674-8 PMID: 18724357
- 4. Shi Q et al.. 2023. Negative Regulation of RIG-I by Tim-3 Promotes H1N1 Infection.. Immunol Invest 52(1):1-19 PMID: 35997714
- 5. Zhou P et al.. 2025. Avian TRIM13 attenuates antiviral innate immunity by targeting MAVS for autophagic degradation.. Autophagy 21(4):754-770 PMID: 39508267
- 6. Li MT et al.. 2013. Negative regulation of RIG-I-mediated innate antiviral signaling by SEC14L1.. J Virol 87(18):10037-46 PMID: 23843640
- 7. Arimoto K et al.. 2007. Negative regulation of the RIG-I signaling by the ubiquitin ligase RNF125.. Proc Natl Acad Sci U S A 104(18):7500-5 PMID: 17460044
- 8. Jena KK et al.. 2020. Autoimmunity gene IRGM suppresses cGAS-STING and RIG-I-MAVS signaling to control interferon response.. EMBO Rep 21(9):e50051 PMID: 32715615
