Interferon-induced helicase C domain-containing protein 1 (IFIH1/MDA5) is a cytosolic RIG-I-like receptor that couples recognition of duplex RNA to type I interferon induction. It has two N-terminal caspase activation and recruitment domains (CARDs), a central DExD/H-box helicase core with an inserted domain, and a zinc-binding C-terminal regulatory domain. Unlike RIG-I, which reads the end of a duplex, MDA5 binds the internal stem of long double-stranded RNA and polymerises head-to-tail along it; ATP binding and hydrolysis drive assembly and disassembly of these filaments, giving a proofreading mechanism that makes signalling depend on duplex length rather than on a chemical mark at the RNA end. Filament formation clusters the CARDs, which nucleate MAVS prion-like polymers on the mitochondrial outer membrane and activate TBK1/IKBKE and IRF3/IRF7, inducing interferon-alpha/beta and pro-inflammatory cytokines; MDA5 itself relocalises from cytosol to mitochondria upon activation and ISGylation. MDA5 is required for the response to picornaviruses such as encephalomyocarditis virus, and contributes to responses to coronaviruses, flaviviruses and some DNA viruses. Which RNA actually engages MDA5 during infection is unresolved. Long viral replicative duplexes and viral mRNA lacking the host 2'-O-methyl cap mark activate it, but crosslinking of endogenous MDA5 in SARS-CoV-2- and encephalomyocarditis-virus-infected cells recovers almost exclusively cellular RNA, concentrated in introns and near inverted Alu repeats, and infection-induced splicing defects are sufficient to trigger it; on that evidence MDA5 has been proposed to monitor the fidelity of host RNA processing rather than to detect a pathogen-specific molecular pattern. The same ambiguity is visible in disease: gain-of-function IFIH1 variants cause Aicardi-Goutieres syndrome and Singleton-Merten-spectrum type I interferonopathies through sterile activation, and adenosine-to-inosine editing by ADAR1 exists in part to prevent MDA5 from responding to endogenous duplex RNA. Common IFIH1 variants are associated with type 1 diabetes and other autoimmune conditions.
Definition: Binding to improperly processed or mislocalised cellular RNA, such as intron-retaining or unspliced transcripts accumulating in the cytoplasm, and thereby initiating an innate immune response. Unlike pattern recognition receptor activity, this activity does not require the bound ligand to be of pathogen origin; the discriminating feature is the processing state of the RNA rather than its provenance.
Justification: GO:0038187 pattern recognition receptor activity is defined as combining with a pathogen-associated molecular pattern. MDA5 is annotated to it, yet the PAMP has never been identified - it is described in the 2026 literature as one of the few remaining 'orphan' PRRs - and crosslinking of endogenous MDA5 in virus-infected cells recovers host rather than viral RNA. Sterile activation in ADAR1 deficiency and in IFIH1 gain-of-function interferonopathies points the same way. There is currently no molecular function term for a receptor that initiates innate immunity by detecting the processing state of self RNA, so curators must either use a term whose definition does not fit or leave the activity unannotated. The same gap affects ZBP1 and OAS1, for which comparable host-RNA and transcription-termination sensing has been reported.
Parent term: double-stranded RNA binding
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0140374 antiviral innate immune response | IBA GO_REF:0000033 | ACCEPT | Summary: MDA5 drives the antiviral innate immune response to picornaviruses, coronaviruses and other agents. Reason: Core biological process, and unaffected by the ligand question: whether MDA5 is triggered by viral RNA or by infection-induced aberrant host RNA, the process it participates in is antiviral innate immunity. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: MDA5 is a cytoplasmic protein. Reason: Correct and consistently observed; this is where the sensor resides and acts. |
| GO:0039530 MDA-5 signaling pathway | IBA GO_REF:0000033 | ACCEPT | Summary: The MDA-5 signalling pathway itself: ligand-bound MDA5 filaments nucleate CARD oligomers that activate MAVS, TBK1/IKBKE and IRF3/IRF7. Reason: Core biological process, named for this gene and supported by independent experimental work. |
| GO:0003725 double-stranded RNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: MDA5 binds long double-stranded RNA and cooperatively assembles head-to-tail filaments along the duplex; this is its core ligand-binding activity. Reason: Core molecular function, established structurally and biochemically and not in dispute. What is disputed is the origin of the duplex RNA that engages MDA5 in infected cells, not the binding activity itself. Sampaio et al. 2026 (PMID:42581186) applied iCLIP to endogenous MDA5 in SARS-CoV-2- and EMCV-infected cells and recovered essentially no viral RNA: the bound population was host RNA, enriched in introns, Alu-proximal regions and predicted duplexes, and MDA5 activation was abolished by SRSF3 overexpression, which restores splicing fidelity. The authors frame MDA5 as surveying RNA processing fidelity ('guarding') rather than detecting a pathogen-encoded pattern, and state plainly that they cannot exclude direct viral dsRNA detection in other settings. This reframes which RNA activates MDA5; it does not challenge the biochemistry of duplex-RNA binding. The host ligands it identifies - inverted Alu repeats and structured intronic RNA - are themselves double-stranded, so this term remains correct under either model. Supporting Evidence: PMID:23273991 MDA5 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. PMID:42581186 upon infection with SARS-CoV-2 or encephalomyocarditis virus, MDA5 bound overwhelmingly to cellular RNAs |
| GO:0003727 single-stranded RNA binding | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Single-stranded RNA binding reported alongside the duplex-binding activity. Reason: Real but peripheral. The signalling-competent ligand for MDA5 is a long duplex bound by a cooperative filament; single-stranded segments are bound within higher-order structures rather than as the activating species. Retained as a genuine binding property, demoted from core. Supporting Evidence: PMID:19656871 Activation of MDA5 requires higher-order RNA structures generated during virus infection. |
| GO:0008270 zinc ion binding | IBA GO_REF:0000033 | ACCEPT | Summary: Zinc coordinated by the C-terminal regulatory domain. Reason: A structural metal site, directly observed, required to fold the domain that caps the RNA duplex. Correct, though architectural rather than a function in its own right. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | REMOVE | Summary: DNA binding assigned electronically from an InterPro signature. Reason: This is an InterPro2GO artefact, not a claim about MDA5. GO_REF:0000002 maps IPR006935 (Helicase/UvrB, N-terminal; Pfam PF04851 ResIII) to GO:0003677, GO:0005524 and GO:0016787, because that domain family is dominated by DNA-acting enzymes such as UvrB and type III restriction endonucleases. MDA5 is a cytosolic RNA sensor: every characterised ligand is RNA, the C-terminal regulatory domain and the helicase core are structurally resolved in complex with dsRNA, and no study reports direct DNA binding by MDA5. MDA5 is activated by some DNA viruses, but the accepted mechanism is indirect, via RNA produced during those infections. Removing an electronic inference that can be argued against on biological grounds; no experimental annotation is being overruled. |
| GO:0003724 RNA helicase activity | IEA GO_REF:0000003 | MODIFY | Summary: RNA helicase activity, defined as ATP-driven unwinding of an RNA helix. MDA5 has a bona fide DExD/H ATPase that is stimulated by duplex RNA, but processive duplex unwinding is not what the ATPase does. Reason: The cited IMP (PMID:19211564) mutated the conserved helicase motifs and measured ATP hydrolysis and signalling, not duplex unwinding, and concluded that interferon induction is independent of helicase catalytic activity. In MDA5 the ATPase powers filament dynamics and length-dependent proofreading. The ATP-hydrolysis term the gene already carries (GO:0016887) states what was measured; 'ATP-dependent activity, acting on RNA' (GO:0008186) captures the RNA-dependence without asserting unwinding. Proposed replacements: ATP-dependent activity, acting on RNA Supporting Evidence: PMID:19211564 type I interferon production mediated by full-length MDA5 and RIG-I is independent of the helicase domain catalytic activity PMID:19211564 Results indicate that all targeted motifs are required for ATP hydrolysis, but a subset is involved in RNA binding. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: ATP binding by the P-loop of the helicase core. Reason: Correct and necessary for the ATPase cycle, though subsidiary to the hydrolysis term. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: Nuclear localisation transferred electronically from the UniProt subcellular-location vocabulary. Reason: UniProt's own nucleus assignment for IFIH1 carries ECO:0000305 (curator inference) and is qualified as 'May be found in the nucleus, during apoptosis'. Propagating that into a plain located_in nucleus annotation overstates it for a protein whose entire characterised biology is cytosolic. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: MDA5 is a cytoplasmic protein. Reason: Correct and consistently observed; this is where the sensor resides and acts. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Mitochondrial localisation observed after activation. Reason: Real but conditional: MDA5 is not a resident mitochondrial protein. Upon ligand binding and ISGylation it translocates to the mitochondrial outer membrane to engage MAVS. Meaningful for signalling, but not a primary location. Supporting Evidence: PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity. |
| GO:0007165 signal transduction | IEA GO_REF:0000117 | MODIFY | Summary: Bare signal transduction from an ARBA machine-learning model. Reason: Correct but far too general; the specific pathway this protein initiates is already annotated. Proposed replacements: MDA-5 signaling pathway |
| GO:0016787 hydrolase activity | IEA GO_REF:0000002 | MODIFY | Summary: Bare hydrolase activity carried over from the InterPro signature IPR006935 (Helicase/UvrB, N-terminal). Reason: Correct in kind but uninformative at this level. The hydrolase activity of MDA5 is ATP hydrolysis, already annotated with experimental evidence. Proposed replacements: ATP hydrolysis activity |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000116 | ACCEPT | Summary: Duplex-RNA-stimulated ATP hydrolysis by the DExD/H helicase core. Reason: Core molecular function. Directly measured, and mechanistically central: ATP turnover drives the assembly/disassembly cycle that discriminates long duplexes from short ones. Supporting Evidence: PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. PMID:19211564 Results indicate that all targeted motifs are required for ATP hydrolysis, but a subset is involved in RNA binding. |
| GO:0051259 protein complex oligomerization | IEA GO_REF:0000117 | ACCEPT | Summary: Protein complex oligomerization: MDA5 filament assembly and CARD oligomerisation. Reason: Directly observed and mechanistically central - the oligomerisation step is how duplex length is converted into a signalling threshold. |
| GO:0140374 antiviral innate immune response | IEA GO_REF:0000117 | ACCEPT | Summary: MDA5 drives the antiviral innate immune response to picornaviruses, coronaviruses and other agents. Reason: Core biological process, and unaffected by the ligand question: whether MDA5 is triggered by viral RNA or by infection-induced aberrant host RNA, the process it participates in is antiviral innate immunity. |
| GO:0005515 protein binding | IPI PMID:17460044 Negative regulation of the RIG-I signaling by the ubiquitin ... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:17600090 Negative regulation of MDA5- but not RIG-I-mediated innate a... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:19403670 A shared interface mediates paramyxovirus interference with ... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:19416887 ISG56 is a negative-feedback regulator of virus-triggered si... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:21903422 Mapping a dynamic innate immunity protein interaction networ... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:22301138 Herpes simplex virus 1 tegument protein US11 downmodulates t... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:22623778 Human respiratory syncytial virus nucleoprotein and inclusio... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:23328395 Paramyxovirus V proteins disrupt the fold of the RNA sensor ... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:25865883 RIOK3-mediated phosphorylation of MDA5 interferes with its a... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:28591694 The nucleocapsid proteins of mouse hepatitis virus and sever... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:31015422 Physical and functional interaction between A20 and ATG16L1-... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:33372174 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:34084167 SARS-CoV-2 Membrane Protein Inhibits Type I Interferon Produ... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0042802 identical protein binding | IPI PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filamen... | ACCEPT | Summary: MDA5 self-association. Filament formation along duplex RNA and CARD-CARD oligomerisation are the mechanism by which ligand binding is converted into a signal. Reason: Unlike bare protein binding, homotypic self-association is mechanistically load-bearing for this protein and is directly observed. Supporting Evidence: PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. |
| GO:0042802 identical protein binding | IPI PMID:25865883 RIOK3-mediated phosphorylation of MDA5 interferes with its a... | ACCEPT | Summary: MDA5 self-association. Filament formation along duplex RNA and CARD-CARD oligomerisation are the mechanism by which ligand binding is converted into a signal. Reason: Unlike bare protein binding, homotypic self-association is mechanistically load-bearing for this protein and is directly observed. Supporting Evidence: PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. |
| GO:0009615 response to virus | IEA GO_REF:0000107 | ACCEPT | Summary: Response to virus. Reason: Correct but general; the gene carries more specific terms (GO:0140374, GO:0051607, GO:0039530) that say the same thing better. |
| GO:0045087 innate immune response | IEA GO_REF:0000107 | ACCEPT | Summary: Innate immune response. Reason: Correct high-level process term. |
| GO:0140374 antiviral innate immune response | IDA PMID:40184173 MDA5 ISGylation is crucial for immune signaling to control v... | ACCEPT | Summary: MDA5 drives the antiviral innate immune response to picornaviruses, coronaviruses and other agents. Reason: Core biological process, and unaffected by the ligand question: whether MDA5 is triggered by viral RNA or by infection-induced aberrant host RNA, the process it participates in is antiviral innate immunity. |
| GO:0005737 cytoplasm | EXP PMID:32169843 NOD1 Promotes Antiviral Signaling by Binding Viral RNA and R... | ACCEPT | Summary: MDA5 is a cytoplasmic protein. Reason: Correct and consistently observed; this is where the sensor resides and acts. |
| GO:0016887 ATP hydrolysis activity | EXP PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filamen... | ACCEPT | Summary: Duplex-RNA-stimulated ATP hydrolysis by the DExD/H helicase core. Reason: Core molecular function. Directly measured, and mechanistically central: ATP turnover drives the assembly/disassembly cycle that discriminates long duplexes from short ones. Supporting Evidence: PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. PMID:19211564 Results indicate that all targeted motifs are required for ATP hydrolysis, but a subset is involved in RNA binding. |
| GO:0005737 cytoplasm | IDA PMID:11805321 mda-5: An interferon-inducible putative RNA helicase with do... | ACCEPT | Summary: MDA5 is a cytoplasmic protein. Reason: Correct and consistently observed; this is where the sensor resides and acts. |
| GO:0038187 pattern recognition receptor activity | IDA PMID:23273991 Structural basis for dsRNA recognition, filament formation, ... | ACCEPT | Summary: Pattern recognition receptor activity: MDA5 binds an RNA ligand and, through its tandem CARDs, initiates MAVS-dependent innate immune signalling. The GO definition requires the ligand to be a pathogen-associated molecular pattern, and that requirement is exactly what the 2026 iCLIP data call into question. Reason: Retained, but this is the annotation on which the contested question turns, and both sides are recorded here rather than resolved. FOR the term: GOA's own supporting experiments are real - Zuest et al. 2011 (PMID:21217758) show MDA5-dependent interferon induction by viral mRNA lacking the host 2'-O-methyl cap mark (self/non-self discrimination), and Wu et al. 2013 (PMID:23273991) show recognition of the internal duplex of long dsRNA, a canonical microbial pattern. AGAINST the term as defined: Sampaio et al. 2026 (PMID:42581186) applied iCLIP to endogenous MDA5 in SARS-CoV-2- and EMCV-infected cells and recovered essentially no viral RNA: the bound population was host RNA, enriched in introns, Alu-proximal regions and predicted duplexes, and MDA5 activation was abolished by SRSF3 overexpression, which restores splicing fidelity. The authors frame MDA5 as surveying RNA processing fidelity ('guarding') rather than detecting a pathogen-encoded pattern, and state plainly that they cannot exclude direct viral dsRNA detection in other settings. This reframes which RNA activates MDA5; it does not challenge the biochemistry of duplex-RNA binding. The same paper calls MDA5 one of the few remaining 'orphan' pattern recognition receptors because no PAMP has been pinned down. Independently, IFIH1 gain-of-function variants cause Aicardi-Goutieres syndrome and related interferonopathies through excessive signalling in the absence of infection (PMID:24686847), and ADAR1 editing exists to stop MDA5 sensing endogenous duplex RNA (PMID:26275108) - both are evidence that the physiological ligand pool includes self RNA distinguished by processing state rather than by pathogen origin. ACCEPT rather than MODIFY or REMOVE because (i) these are IDA annotations whose full experimental basis stands, and (ii) the mismatch is with the wording of GO:0038187, not with this gene: no existing MF term describes a receptor that senses aberrantly processed cellular RNA. A replacement term is proposed under proposed_new_terms and the question is raised in suggested_questions rather than being settled by an edit here. Supporting Evidence: PMID:21217758 the induction of type I interferon by viruses deficient in 2'-O-methyltransferase was dependent on the cytoplasmic RNA sensor Mda5 PMID:42581186 We did not detect MDA5 binding sites in viral RNA; instead, MDA5 bound only host RNA. PMID:42581186 MDA5's RNA agonists are not well defined. PMID:24686847 these mutations confer gain of function such that mutant IFIH1 binds RNA more avidly, leading to increased baseline and ligand-induced interferon signaling |
| GO:0005737 cytoplasm | IDA PMID:28031478 TRIM65-catalized ubiquitination is essential for MDA5-mediat... | ACCEPT | Summary: MDA5 is a cytoplasmic protein. Reason: Correct and consistently observed; this is where the sensor resides and acts. |
| GO:0019904 protein domain specific binding | IPI PMID:28031478 TRIM65-catalized ubiquitination is essential for MDA5-mediat... | MARK AS OVER ANNOTATED | Summary: Protein domain specific binding from a two-hybrid/interaction study. Reason: As uninformative as bare protein binding; it names no partner and no function. |
| GO:0051259 protein complex oligomerization | IDA PMID:28031478 TRIM65-catalized ubiquitination is essential for MDA5-mediat... | ACCEPT | Summary: Protein complex oligomerization: MDA5 filament assembly and CARD oligomerisation. Reason: Directly observed and mechanistically central - the oligomerisation step is how duplex length is converted into a signalling threshold. |
| GO:0009615 response to virus | IDA PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized... | ACCEPT | Summary: Response to virus. Reason: Correct but general; the gene carries more specific terms (GO:0140374, GO:0051607, GO:0039530) that say the same thing better. |
| GO:0003724 RNA helicase activity | IMP PMID:19211564 Regulation of signal transduction by enzymatically inactive ... | MODIFY | Summary: RNA helicase activity, defined as ATP-driven unwinding of an RNA helix. MDA5 has a bona fide DExD/H ATPase that is stimulated by duplex RNA, but processive duplex unwinding is not what the ATPase does. Reason: The cited IMP (PMID:19211564) mutated the conserved helicase motifs and measured ATP hydrolysis and signalling, not duplex unwinding, and concluded that interferon induction is independent of helicase catalytic activity. In MDA5 the ATPase powers filament dynamics and length-dependent proofreading. The ATP-hydrolysis term the gene already carries (GO:0016887) states what was measured; 'ATP-dependent activity, acting on RNA' (GO:0008186) captures the RNA-dependence without asserting unwinding. Proposed replacements: ATP-dependent activity, acting on RNA Supporting Evidence: PMID:19211564 type I interferon production mediated by full-length MDA5 and RIG-I is independent of the helicase domain catalytic activity PMID:19211564 Results indicate that all targeted motifs are required for ATP hydrolysis, but a subset is involved in RNA binding. |
| GO:0016887 ATP hydrolysis activity | IMP PMID:19211564 Regulation of signal transduction by enzymatically inactive ... | ACCEPT | Summary: Duplex-RNA-stimulated ATP hydrolysis by the DExD/H helicase core. Reason: Core molecular function. Directly measured, and mechanistically central: ATP turnover drives the assembly/disassembly cycle that discriminates long duplexes from short ones. Supporting Evidence: PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. PMID:19211564 Results indicate that all targeted motifs are required for ATP hydrolysis, but a subset is involved in RNA binding. |
| GO:0039530 MDA-5 signaling pathway | IMP PMID:19211564 Regulation of signal transduction by enzymatically inactive ... | ACCEPT | Summary: The MDA-5 signalling pathway itself: ligand-bound MDA5 filaments nucleate CARD oligomers that activate MAVS, TBK1/IKBKE and IRF3/IRF7. Reason: Core biological process, named for this gene and supported by independent experimental work. |
| GO:0003723 RNA binding | IDA PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized... | MODIFY | Summary: Bare RNA binding. Reason: Correct but too general for a protein whose RNA-binding specificity is the whole point. The duplex-binding term is the informative one and the gene already carries it with independent experimental support. Proposed replacements: double-stranded RNA binding |
| GO:0005737 cytoplasm | IDA PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized... | ACCEPT | Summary: MDA5 is a cytoplasmic protein. Reason: Correct and consistently observed; this is where the sensor resides and acts. |
| GO:0005739 mitochondrion | IDA PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized... | KEEP AS NON CORE | Summary: Mitochondrial localisation observed after activation. Reason: Real but conditional: MDA5 is not a resident mitochondrial protein. Upon ligand binding and ISGylation it translocates to the mitochondrial outer membrane to engage MAVS. Meaningful for signalling, but not a primary location. Supporting Evidence: PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity. |
| GO:0032728 positive regulation of interferon-beta production | IDA PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized... | ACCEPT | Summary: Positive regulation of interferon-beta production. Reason: Core biological output of the pathway, with multiple independent experimental annotations. |
| GO:0039530 MDA-5 signaling pathway | IDA PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized... | ACCEPT | Summary: The MDA-5 signalling pathway itself: ligand-bound MDA5 filaments nucleate CARD oligomers that activate MAVS, TBK1/IKBKE and IRF3/IRF7. Reason: Core biological process, named for this gene and supported by independent experimental work. |
| GO:0042802 identical protein binding | IDA PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized... | ACCEPT | Summary: MDA5 self-association. Filament formation along duplex RNA and CARD-CARD oligomerisation are the mechanism by which ligand binding is converted into a signal. Reason: Unlike bare protein binding, homotypic self-association is mechanistically load-bearing for this protein and is directly observed. Supporting Evidence: PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. |
| GO:0045071 negative regulation of viral genome replication | IDA PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized... | KEEP AS NON CORE | Summary: Negative regulation of viral genome replication. Reason: A true consequence of MDA5-driven interferon induction, but effected by interferon-stimulated genes rather than by MDA5 itself. |
| GO:0051607 defense response to virus | IDA PMID:33727702 ISG15-dependent activation of the sensor MDA5 is antagonized... | ACCEPT | Summary: Defense response to virus. Reason: Correct and experimentally supported. |
| GO:0098586 cellular response to virus | IEP PMID:28146100 Echovirus 6 Infects Human Exocrine and Endocrine Pancreatic ... | ACCEPT | Summary: Cellular response to virus, from expression evidence. Reason: Correct; IFIH1 is itself an interferon-stimulated gene and is induced by infection. |
| GO:0042802 identical protein binding | IDA PMID:23090998 MDA5 assembles into a polar helical filament on dsRNA. | ACCEPT | Summary: MDA5 self-association. Filament formation along duplex RNA and CARD-CARD oligomerisation are the mechanism by which ligand binding is converted into a signal. Reason: Unlike bare protein binding, homotypic self-association is mechanistically load-bearing for this protein and is directly observed. Supporting Evidence: PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. |
| GO:0042802 identical protein binding | IDA PMID:30449722 Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stag... | ACCEPT | Summary: MDA5 self-association. Filament formation along duplex RNA and CARD-CARD oligomerisation are the mechanism by which ligand binding is converted into a signal. Reason: Unlike bare protein binding, homotypic self-association is mechanistically load-bearing for this protein and is directly observed. Supporting Evidence: PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. |
| GO:0038187 pattern recognition receptor activity | IDA PMID:21217758 Ribose 2'-O-methylation provides a molecular signature for t... | ACCEPT | Summary: Pattern recognition receptor activity: MDA5 binds an RNA ligand and, through its tandem CARDs, initiates MAVS-dependent innate immune signalling. The GO definition requires the ligand to be a pathogen-associated molecular pattern, and that requirement is exactly what the 2026 iCLIP data call into question. Reason: Retained, but this is the annotation on which the contested question turns, and both sides are recorded here rather than resolved. FOR the term: GOA's own supporting experiments are real - Zuest et al. 2011 (PMID:21217758) show MDA5-dependent interferon induction by viral mRNA lacking the host 2'-O-methyl cap mark (self/non-self discrimination), and Wu et al. 2013 (PMID:23273991) show recognition of the internal duplex of long dsRNA, a canonical microbial pattern. AGAINST the term as defined: Sampaio et al. 2026 (PMID:42581186) applied iCLIP to endogenous MDA5 in SARS-CoV-2- and EMCV-infected cells and recovered essentially no viral RNA: the bound population was host RNA, enriched in introns, Alu-proximal regions and predicted duplexes, and MDA5 activation was abolished by SRSF3 overexpression, which restores splicing fidelity. The authors frame MDA5 as surveying RNA processing fidelity ('guarding') rather than detecting a pathogen-encoded pattern, and state plainly that they cannot exclude direct viral dsRNA detection in other settings. This reframes which RNA activates MDA5; it does not challenge the biochemistry of duplex-RNA binding. The same paper calls MDA5 one of the few remaining 'orphan' pattern recognition receptors because no PAMP has been pinned down. Independently, IFIH1 gain-of-function variants cause Aicardi-Goutieres syndrome and related interferonopathies through excessive signalling in the absence of infection (PMID:24686847), and ADAR1 editing exists to stop MDA5 sensing endogenous duplex RNA (PMID:26275108) - both are evidence that the physiological ligand pool includes self RNA distinguished by processing state rather than by pathogen origin. ACCEPT rather than MODIFY or REMOVE because (i) these are IDA annotations whose full experimental basis stands, and (ii) the mismatch is with the wording of GO:0038187, not with this gene: no existing MF term describes a receptor that senses aberrantly processed cellular RNA. A replacement term is proposed under proposed_new_terms and the question is raised in suggested_questions rather than being settled by an edit here. Supporting Evidence: PMID:21217758 the induction of type I interferon by viruses deficient in 2'-O-methyltransferase was dependent on the cytoplasmic RNA sensor Mda5 PMID:42581186 We did not detect MDA5 binding sites in viral RNA; instead, MDA5 bound only host RNA. PMID:42581186 MDA5's RNA agonists are not well defined. PMID:24686847 these mutations confer gain of function such that mutant IFIH1 binds RNA more avidly, leading to increased baseline and ligand-induced interferon signaling |
| GO:0140374 antiviral innate immune response | IDA PMID:15563593 The V proteins of paramyxoviruses bind the IFN-inducible RNA... | ACCEPT | Summary: MDA5 drives the antiviral innate immune response to picornaviruses, coronaviruses and other agents. Reason: Core biological process, and unaffected by the ligand question: whether MDA5 is triggered by viral RNA or by infection-induced aberrant host RNA, the process it participates in is antiviral innate immunity. |
| GO:0005515 protein binding | IPI PMID:30193849 The Zinc-Finger Protein ZCCHC3 Binds RNA and Facilitates Vir... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0051607 defense response to virus | IDA PMID:21478870 A diverse range of gene products are effectors of the type I... | ACCEPT | Summary: Defense response to virus. Reason: Correct and experimentally supported. |
| GO:0032727 positive regulation of interferon-alpha production | IMP PMID:21957149 DHX9 pairs with IPS-1 to sense double-stranded RNA in myeloi... | ACCEPT | Summary: Positive regulation of interferon-alpha production. Reason: Direct downstream output of MDA5 signalling, supported by loss-of-function experiments. |
| GO:0032728 positive regulation of interferon-beta production | IMP PMID:21957149 DHX9 pairs with IPS-1 to sense double-stranded RNA in myeloi... | ACCEPT | Summary: Positive regulation of interferon-beta production. Reason: Core biological output of the pathway, with multiple independent experimental annotations. |
| GO:0032755 positive regulation of interleukin-6 production | IMP PMID:21957149 DHX9 pairs with IPS-1 to sense double-stranded RNA in myeloi... | KEEP AS NON CORE | Summary: Positive regulation of interleukin-6 production. Reason: A downstream inflammatory consequence of MDA5-MAVS signalling rather than a distinct activity of the protein. |
| GO:0032760 positive regulation of tumor necrosis factor production | IMP PMID:21957149 DHX9 pairs with IPS-1 to sense double-stranded RNA in myeloi... | KEEP AS NON CORE | Summary: Positive regulation of tumor necrosis factor production. Reason: A downstream inflammatory consequence of MDA5-MAVS signalling rather than a distinct activity of the protein. |
| GO:0060760 positive regulation of response to cytokine stimulus | IMP PMID:21957149 DHX9 pairs with IPS-1 to sense double-stranded RNA in myeloi... | KEEP AS NON CORE | Summary: Positive regulation of response to cytokine stimulus. Reason: Distal and non-specific; a consequence of the interferon amplification loop. |
| GO:0071360 cellular response to exogenous dsRNA | IMP PMID:21957149 DHX9 pairs with IPS-1 to sense double-stranded RNA in myeloi... | ACCEPT | Summary: Cellular response to exogenous double-stranded RNA. Reason: Correct and directly tested: transfected dsRNA activates MDA5-dependent signalling. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-5696600 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0032728 positive regulation of interferon-beta production | IDA PMID:17600090 Negative regulation of MDA5- but not RIG-I-mediated innate a... | ACCEPT | Summary: Positive regulation of interferon-beta production. Reason: Core biological output of the pathway, with multiple independent experimental annotations. |
| GO:0039530 MDA-5 signaling pathway | IDA PMID:17600090 Negative regulation of MDA5- but not RIG-I-mediated innate a... | ACCEPT | Summary: The MDA-5 signalling pathway itself: ligand-bound MDA5 filaments nucleate CARD oligomers that activate MAVS, TBK1/IKBKE and IRF3/IRF7. Reason: Core biological process, named for this gene and supported by independent experimental work. |
| GO:0005515 protein binding | IPI PMID:22328336 Ankrd17 positively regulates RIG-I-like receptor (RLR)-media... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:22908223 Tetraspanin 6 (TSPAN6) negatively regulates retinoic acid-in... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-168909 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-168934 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-913725 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-918225 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-918227 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-918229 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-918230 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-918232 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-933523 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-933525 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-933526 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-933527 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-933530 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-933532 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-933537 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-933538 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-933539 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-936381 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-936475 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-937343 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9705137 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9705145 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9705320 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9705323 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9754745 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9755244 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9833393 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-990526 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-990528 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9920772 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9924831 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-NUL-936401 | ACCEPT | Summary: Cytosolic localisation, asserted by Reactome pathway curation. Reason: Correct and more specific than bare cytoplasm. |
| GO:0005515 protein binding | IPI PMID:21791617 DDX60, a DEXD/H box helicase, is a novel antiviral factor pr... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0002753 cytoplasmic pattern recognition receptor signaling pathway | TAS PMID:21616437 Immune signaling by RIG-I-like receptors. | ACCEPT | Summary: Cytoplasmic pattern recognition receptor signalling pathway, the parent of the MDA-5 pathway. Reason: Correct as the general pathway class. Its definition inherits the same PAMP wording as GO:0038187 and inherits the same caveat, recorded there; the specific child term GO:0039530 is the informative annotation. |
| GO:0003725 double-stranded RNA binding | IDA PMID:19656871 Activation of MDA5 requires higher-order RNA structures gene... | ACCEPT | Summary: MDA5 binds long double-stranded RNA and cooperatively assembles head-to-tail filaments along the duplex; this is its core ligand-binding activity. Reason: Core molecular function, established structurally and biochemically and not in dispute. What is disputed is the origin of the duplex RNA that engages MDA5 in infected cells, not the binding activity itself. Sampaio et al. 2026 (PMID:42581186) applied iCLIP to endogenous MDA5 in SARS-CoV-2- and EMCV-infected cells and recovered essentially no viral RNA: the bound population was host RNA, enriched in introns, Alu-proximal regions and predicted duplexes, and MDA5 activation was abolished by SRSF3 overexpression, which restores splicing fidelity. The authors frame MDA5 as surveying RNA processing fidelity ('guarding') rather than detecting a pathogen-encoded pattern, and state plainly that they cannot exclude direct viral dsRNA detection in other settings. This reframes which RNA activates MDA5; it does not challenge the biochemistry of duplex-RNA binding. The host ligands it identifies - inverted Alu repeats and structured intronic RNA - are themselves double-stranded, so this term remains correct under either model. Supporting Evidence: PMID:23273991 MDA5 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. PMID:42581186 upon infection with SARS-CoV-2 or encephalomyocarditis virus, MDA5 bound overwhelmingly to cellular RNAs |
| GO:0003727 single-stranded RNA binding | IDA PMID:19656871 Activation of MDA5 requires higher-order RNA structures gene... | KEEP AS NON CORE | Summary: Single-stranded RNA binding reported alongside the duplex-binding activity. Reason: Real but peripheral. The signalling-competent ligand for MDA5 is a long duplex bound by a cooperative filament; single-stranded segments are bound within higher-order structures rather than as the activating species. Retained as a genuine binding property, demoted from core. Supporting Evidence: PMID:19656871 Activation of MDA5 requires higher-order RNA structures generated during virus infection. |
| GO:0005515 protein binding | IPI PMID:21156324 MDA5 is SUMOylated by PIAS2Ξ² in the upregulation of type I i... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0009615 response to virus | TAS PMID:21616437 Immune signaling by RIG-I-like receptors. | ACCEPT | Summary: Response to virus. Reason: Correct but general; the gene carries more specific terms (GO:0140374, GO:0051607, GO:0039530) that say the same thing better. |
| GO:0016925 protein sumoylation | IDA PMID:21156324 MDA5 is SUMOylated by PIAS2Ξ² in the upregulation of type I i... | MARK AS OVER ANNOTATED | Summary: Protein sumoylation, annotated involved_in. Reason: MDA5 is the substrate of SUMO conjugation, not a participant in the sumoylation machinery. An involved_in annotation on a modified substrate misstates the direction of the relationship. |
| GO:0032727 positive regulation of interferon-alpha production | IMP PMID:19656871 Activation of MDA5 requires higher-order RNA structures gene... | ACCEPT | Summary: Positive regulation of interferon-alpha production. Reason: Direct downstream output of MDA5 signalling, supported by loss-of-function experiments. |
| GO:0032728 positive regulation of interferon-beta production | IMP PMID:19656871 Activation of MDA5 requires higher-order RNA structures gene... | ACCEPT | Summary: Positive regulation of interferon-beta production. Reason: Core biological output of the pathway, with multiple independent experimental annotations. |
| GO:0034344 regulation of type III interferon production | TAS PMID:21616437 Immune signaling by RIG-I-like receptors. | KEEP AS NON CORE | Summary: Regulation of type III interferon production. Reason: Real but secondary to the type I interferon output that defines the pathway. |
| GO:0045087 innate immune response | TAS PMID:21616437 Immune signaling by RIG-I-like receptors. | ACCEPT | Summary: Innate immune response. Reason: Correct high-level process term. |
| GO:0003725 double-stranded RNA binding | TAS PMID:17079289 Inhibition of retinoic acid-inducible gene I-mediated induct... | ACCEPT | Summary: MDA5 binds long double-stranded RNA and cooperatively assembles head-to-tail filaments along the duplex; this is its core ligand-binding activity. Reason: Core molecular function, established structurally and biochemically and not in dispute. What is disputed is the origin of the duplex RNA that engages MDA5 in infected cells, not the binding activity itself. Sampaio et al. 2026 (PMID:42581186) applied iCLIP to endogenous MDA5 in SARS-CoV-2- and EMCV-infected cells and recovered essentially no viral RNA: the bound population was host RNA, enriched in introns, Alu-proximal regions and predicted duplexes, and MDA5 activation was abolished by SRSF3 overexpression, which restores splicing fidelity. The authors frame MDA5 as surveying RNA processing fidelity ('guarding') rather than detecting a pathogen-encoded pattern, and state plainly that they cannot exclude direct viral dsRNA detection in other settings. This reframes which RNA activates MDA5; it does not challenge the biochemistry of duplex-RNA binding. The host ligands it identifies - inverted Alu repeats and structured intronic RNA - are themselves double-stranded, so this term remains correct under either model. Supporting Evidence: PMID:23273991 MDA5 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA PMID:22160685 Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. PMID:42581186 upon infection with SARS-CoV-2 or encephalomyocarditis virus, MDA5 bound overwhelmingly to cellular RNAs |
| GO:0009597 detection of virus | TAS PMID:17079289 Inhibition of retinoic acid-inducible gene I-mediated induct... | KEEP AS NON CORE | Summary: Detection of virus, from a review article. Reason: Retained as a fair description of the physiological outcome, but this is the BP term most exposed to the ligand question: the 2026 iCLIP data indicate that in infected cells MDA5 occupies host rather than viral RNA, so what is detected may be the infection's effect on RNA processing rather than the virus itself. Demoted from core; GO:0140374 and GO:0039530 carry the same biology without the mechanistic commitment. Supporting Evidence: PMID:42581186 we propose that MDA5 surveys RNA processing fidelity and can detect infections by sensing perturbations of post-transcriptional events such as splicing. |
| GO:0032727 positive regulation of interferon-alpha production | TAS PMID:17079289 Inhibition of retinoic acid-inducible gene I-mediated induct... | ACCEPT | Summary: Positive regulation of interferon-alpha production. Reason: Direct downstream output of MDA5 signalling, supported by loss-of-function experiments. |
| GO:0032728 positive regulation of interferon-beta production | TAS PMID:17079289 Inhibition of retinoic acid-inducible gene I-mediated induct... | ACCEPT | Summary: Positive regulation of interferon-beta production. Reason: Core biological output of the pathway, with multiple independent experimental annotations. |
| GO:0005515 protein binding | IPI PMID:16127453 IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:20434986 NLRC5 negatively regulates the NF-kappaB and type I interfer... | REMOVE | Summary: Bare protein binding from interaction screens. Reason: Carries no functional information. Per project guidance, a specific molecular function term should be used instead where one is available. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0043021 ribonucleoprotein complex binding | IPI PMID:19881509 PCBP2 mediates degradation of the adaptor MAVS via the HECT ... | KEEP AS NON CORE | Summary: Binding to a ribonucleoprotein complex. Reason: Plausible and consistent with MDA5 engaging RNA that is already protein-bound - a point the 2026 iCLIP work makes explicitly, proposing that host RNA-binding proteins relocalised to the cytoplasm may deliver unspliced RNA to MDA5 - but peripheral to the core function. |
| GO:0008270 zinc ion binding | IDA PMID:19380577 Solution structures of cytosolic RNA sensor MDA5 and LGP2 C-... | ACCEPT | Summary: Zinc coordinated by the C-terminal regulatory domain. Reason: A structural metal site, directly observed, required to fold the domain that caps the RNA duplex. Correct, though architectural rather than a function in its own right. |
| GO:0008270 zinc ion binding | IDA PMID:19531363 Structural basis of double-stranded RNA recognition by the R... | ACCEPT | Summary: Zinc coordinated by the C-terminal regulatory domain. Reason: A structural metal site, directly observed, required to fold the domain that caps the RNA duplex. Correct, though architectural rather than a function in its own right. |
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Download this section (compressed HTML)Q: Should IFIH1 keep GO:0038187 pattern recognition receptor activity, whose definition requires the ligand to be a pathogen-associated molecular pattern, when the RNA occupied by endogenous MDA5 during SARS-CoV-2 and EMCV infection is host-derived, and when the activating signal can be removed simply by restoring splicing fidelity with SRSF3? Or does GO need a molecular function term for a receptor that reads the processing state of self RNA?
Suggested experts: GO innate immunity curators, Jan Rehwinkel, Sun Hur
Q: Are the viral-ligand results and the host-RNA results in conflict, or are they measuring different things? Purified MDA5 demonstrably binds long viral duplexes and unmethylated viral mRNA in vitro, while iCLIP measures which RNAs MDA5 is crosslinked to in an infected cell, where viral RNA may be sequestered in replication organelles and coated by viral proteins. A direct test would be whether MDA5 activation survives in cells where host splicing is protected but viral replication proceeds normally.
Suggested experts: Jan Rehwinkel, Sun Hur, Michaela Gack
Q: If MDA5 is a guard rather than a PAMP receptor, is the gain-of-function interferonopathy phenotype better described as loss of a threshold on normal self-RNA surveillance than as inappropriate self recognition? That distinction matters for how the Aicardi-Goutieres and Singleton-Merten alleles should be annotated with respect to this gene's normal function.
Suggested experts: Yanick Crow, Sun Hur
Q: Does MDA5 have any physiologically relevant duplex-unwinding activity? GO:0003724 RNA helicase activity asserts ATP-driven unwinding of an RNA helix, but the IMP behind it measured ATP hydrolysis and signalling, and concluded that helicase catalytic activity is dispensable for interferon induction.
Suggested experts: Sun Hur, Anna Marie Pyle
Experiment: Uncouple viral replication from host RNA-processing failure. In MDA5-competent cells, infect with EMCV or SARS-CoV-2 while restoring splicing fidelity (SRSF3 overexpression, or complementation of the virus-encoded splicing antagonist) and measure IFNB1 induction, CARD oligomerisation and MDA5 filament formation. Conversely, induce intron retention pharmacologically in the absence of infection and ask whether MDA5 is activated to the same extent. A clean dissociation in either direction would settle whether the activating ligand is viral.
Hypothesis: MDA5 activation during infection requires accumulation of unspliced or aberrantly processed host transcripts in the cytoplasm, and is not triggered by viral RNA per se.
Type: infection plus splicing-modulation, with interferon and MDA5 oligomerisation readouts
Experiment: Apply the published endogenous-MDA5 iCLIP protocol to uninfected patient-derived cells carrying AGS/Singleton-Merten IFIH1 alleles and to ADAR1-deficient cells, and compare the bound RNA populations with those recovered from infected wild-type cells. Overlap in intronic and inverted-Alu binding sites would argue that infection and interferonopathy converge on one ligand class, which would in turn argue that the molecular function term should not presuppose pathogen origin.
Hypothesis: The RNAs bound by MDA5 in gain-of-function interferonopathy patients are the same aberrantly processed host transcripts identified during infection.
Type: iCLIP on patient-derived and ADAR1-deficient cells
Experiment: Run side-by-side single-molecule unwinding assays on purified full-length MDA5 and on a bona fide processive RNA helicase using identical duplex substrates and ATP concentrations, and compare with filament assembly/disassembly kinetics on the same substrates. A clear absence of unwinding would justify replacing GO:0003724 with a term that asserts ATP-dependent activity on RNA without asserting unwinding.
Hypothesis: MDA5 does not unwind RNA duplexes processively; its ATPase serves filament proofreading only.
Type: single-molecule helicase assay
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