Interferon regulatory factor 9 (IRF9; ISGF3 gamma, p48) is a member of the IRF family of transcription factors, with an N-terminal tryptophan-repeat IRF DNA-binding domain and a C-terminal IRF-association domain (IAD). IRF9 is the DNA-recognition subunit of the interferon-stimulated gene factor 3 (ISGF3) complex. After type I interferon stimulation, JAK-mediated tyrosine phosphorylation of STAT1 and STAT2 allows the STAT1:STAT2 heterodimer to associate with IRF9, which binds the STAT2 coiled-coil domain through its IAD. The ternary complex accumulates in the nucleus and binds IFN-stimulated response elements (ISREs) to activate transcription of interferon-stimulated genes that establish an antiviral state. IRF9 is found in both cytoplasm and nucleus, with a basal nuclear pool. Elevated levels of unphosphorylated STAT1, STAT2 and IRF9 can form an unphosphorylated ISGF3 that sustains expression of a subset of ISGs. Biallelic loss-of-function IRF9 variants cause an autosomal recessive immunodeficiency (IMD65) with severe viral infections, notably life-threatening influenza pneumonitis, reflecting loss of ISGF3-dependent responses.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000785 chromatin | ISA GO_REF:0000113 | ACCEPT | Summary: TFClass-based assignment of chromatin location to IRF9 as a sequence-specific DbTF. ChIP shows IRF9-containing ISGF3 on ISREs in ISG promoters. Reason: IRF9 binds ISRE elements in chromatin as part of ISGF3; ChIP in human cells places IRF9 at ISG promoters (PMID:24065129). Supporting Evidence: PMID:24065129 We conclude that the amount of the ternary U-ISGF3 complex is increased in response to high levels of U-STAT1, U-STAT2, and IRF9 without IFN-induced phosphorylation and is present on ISREs in the promoters of U-ISGF3 target genes |
| GO:0000976 transcription cis-regulatory region binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the IRF DNA-binding domain (IPR001346). True, but less specific than the ISRE (RNA polymerase II cis-regulatory) sequence-specific binding that IRF9 is shown to have. Reason: Correct but general. The gene already carries GO:0000978 (accepted here), a descendant that captures the sequence-specific ISRE binding established for human IRF9 (PMID:1630447, PMID:30143481). Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:1630447 ISGF3 gamma serves as the DNA recognition subunit PMID:30143481 Electrophoretic mobility shift assays (EMSAs) confirmed that Pβs cells were not able to form a functional ISGF3 complex following IFN-Ξ±2b stimulation, as evidenced by abolished ISRE binding in vitro |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT node PTN000942746 propagates sequence-specific RNAPII cis-regulatory DNA binding across the IRF family; human IRF9 is itself among the experimental donors. IRF9 is the DNA-recognition subunit of ISGF3 that binds ISREs. Reason: Consistent with direct biochemical evidence for human IRF9 (ISGF3 gamma) as the ISRE DNA-recognition subunit, and loss of ISRE binding in IRF9-deficient patient cells. Supporting Evidence: PMID:1630447 ISGF3 gamma serves as the DNA recognition subunit PMID:30143481 Electrophoretic mobility shift assays (EMSAs) confirmed that Pβs cells were not able to form a functional ISGF3 complex following IFN-Ξ±2b stimulation, as evidenced by abolished ISRE binding in vitro |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA-based electronic annotation of RNAPII cis-regulatory sequence-specific DNA binding. Reason: Agrees with experimental evidence that IRF9 is the ISRE-binding subunit of ISGF3 (PMID:1630447, PMID:30143481). Supporting Evidence: PMID:1630447 ISGF3 gamma serves as the DNA recognition subunit PMID:30143481 Electrophoretic mobility shift assays (EMSAs) confirmed that Pβs cells were not able to form a functional ISGF3 complex following IFN-Ξ±2b stimulation, as evidenced by abolished ISRE binding in vitro |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IMP PMID:24882218 Unanchored K48-linked polyubiquitin synthesized by the E3-ub... | ACCEPT | Summary: IMP annotation from the TRIM6/IKKepsilon study (PMID:24882218). The cached text of this paper is truncated to the introduction, so the specific IRF9 experiment cannot be inspected; the introduction restates the ISGF3 role. Reason: The activity is well established for human IRF9 by independent evidence (PMID:1630447, PMID:30143481); deferring to the curator who read the full text. Supporting Evidence: PMID:24882218 Together STAT1, STAT2, and a third transcription factor, IRF9, form the Interferon Stimulated Gene Factor 3 (ISGF3) complex, which is essential for induction of many IFN stimulated genes (ISGs) PMID:1630447 ISGF3 gamma serves as the DNA recognition subunit PMID:30143481 Electrophoretic mobility shift assays (EMSAs) confirmed that Pβs cells were not able to form a functional ISGF3 complex following IFN-Ξ±2b stimulation, as evidenced by abolished ISRE binding in vitro |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT (PTN000942746) propagates RNAPII-specific DbTF activity across IRF family members. IRF9 provides the DNA-binding activity of the ISGF3 transcription factor, which activates ISRE-containing genes. Reason: IRF9 is the DNA-binding component of ISGF3, and ISRE-dependent transcription is abolished with mutant IRF9 (PMID:30143481). Within ISGF3 the strong transactivation domain is contributed by STAT2, so IRF9 acts as the DNA-targeting subunit of the active transcription factor; the term is still appropriate for the gene product. Supporting Evidence: PMID:1630447 ISGF3 gamma serves as the DNA recognition subunit PMID:30143481 U2A cells transfected with IRF9-Ξex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter Reactome:R-HSA-909721 IRF9 is the DNA binding part of this ISGF3 complex |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | ISA GO_REF:0000113 | ACCEPT | Summary: TFClass-based assignment of IRF9 to the sequence-specific DbTF class (IRF family, tfclass:3.5.3). Reason: Consistent with experimental evidence that IRF9 binds ISREs and is required for ISRE-driven transcription (PMID:1630447, PMID:30143481). Supporting Evidence: PMID:1630447 ISGF3 gamma serves as the DNA recognition subunit PMID:30143481 U2A cells transfected with IRF9-Ξex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter |
| GO:0002376 immune system process | IBA GO_REF:0000033 | MODIFY | Summary: PAINT node PTN000942747 propagates immune system process across IRF family members. IRF9 does act in innate antiviral immunity, specifically as the DNA-binding subunit of the type I interferon effector complex ISGF3. Reason: The term is correct but very general. The specific process in which IRF9 does the work is type I interferon-mediated signaling, where it targets ISGF3 to ISREs (PMID:30143481). GO:0060337 is proposed as the informative replacement (also added as NEW below). Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000942747 SUPPORTS TRANSFER IRF-family node; immune system process is a sound family-level transfer, and the IRF9-specific refinement is type I interferon-mediated signaling. Proposed replacements: type I interferon-mediated signaling pathway Supporting Evidence: PMID:30143481 Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-Ξ±2b PMID:30143481 These phenotypes are rescued by wild-type IRF9, whereas silencing IRF9 expression in control cells increases viral replication |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000120 | MODIFY | Summary: Combined InterPro/ARBA electronic mapping to generic DbTF activity. Reason: Correct but general; the gene already carries the RNAPII-specific child GO:0000981 (accepted), which matches the ISRE-driven RNAPII transcription controlled by ISGF3. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:1630447 ISGF3 gamma serves as the DNA recognition subunit PMID:30143481 U2A cells transfected with IRF9-Ξex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter |
| GO:0003700 DNA-binding transcription factor activity | TAS PMID:1630447 Subunit of an alpha-interferon-responsive transcription fact... | MODIFY | Summary: TAS from the original cloning of ISGF3 gamma (PMID:1630447), which identified it as the DNA recognition subunit of an IFN-alpha-responsive transcription factor. Reason: Correct but general; refine to the RNAPII-specific child GO:0000981 that the gene already carries, as ISGF3 targets RNAPII-transcribed ISGs. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:1630447 ISGF3 gamma serves as the DNA recognition subunit PMID:1630447 Recombinant ISGF3 gamma, like the natural protein, interacted with HeLa cell ISGF3 alpha to form the mature ISGF3 DNA-binding complex |
| GO:0005515 protein binding | IPI PMID:17923090 Acetylation-dependent signal transduction for type I interfe... | MODIFY | Summary: IPI with IFNAR2 (P48551). The abstract reports that IRF9 docks, via its IH2/IAD domain, on CBP-acetylated Lys399 of the IFNAR2 cytoplasmic tail. Reason: Generic protein binding is uninformative; the paper supports binding to a cytokine receptor subunit. This acetylation-dependent docking model comes from a single study (abstract only in cache), so the replacement is regarded as non-core. Proposed replacements: cytokine receptor binding Supporting Evidence: PMID:17923090 IRF9 interacts with the acetyl-Lys399 motif by means of its IRF homology2 (IH2) domain, leading to formation of the ISGF3 complex that includes IRF9, STAT1, and STAT2 |
| GO:0005515 protein binding | IPI PMID:17923090 Acetylation-dependent signal transduction for type I interfe... | MODIFY | Summary: IPI with STAT2 (P52630), a DNA-binding transcription factor. IRF9 binds STAT2 through its IRF-association domain (IAD) and the STAT2 coiled-coil domain, forming ISGF3. Reason: Generic protein binding is uninformative. The interaction is with a DNA-binding transcription factor and is the structural basis of ISGF3 assembly (PMID:29317535), so DNA-binding transcription factor binding is the informative replacement. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:17923090 IRF9 interacts with the acetyl-Lys399 motif by means of its IRF homology2 (IH2) domain, leading to formation of the ISGF3 complex that includes IRF9, STAT1, and STAT2 PMID:29317535 ISGF3 function depends on selective interaction between IRF9, through its IRF-association domain (IAD), with the coiled-coil domain (CCD) of STAT2 |
| GO:0005515 protein binding | IPI PMID:21903422 Mapping a dynamic innate immunity protein interaction networ... | REMOVE | Summary: High-throughput interaction screen reporting IRF9 with STAT2 (P52630). The IRF9-STAT2 interaction is real and central to IRF9 function, but generic protein binding is uninformative; the interaction is captured more informatively by the DNA-binding transcription factor binding replacement on the low-throughput STAT2 rows and by the ISGF3 complex annotation. Reason: Generic GO:0005515 from a high-throughput interactome study is uninformative per project protein-binding policy; removal does not dispute the IRF9-STAT2 interaction, which is captured by GO:0140297 and GO:0070721. Supporting Evidence: PMID:29317535 ISGF3 function depends on selective interaction between IRF9, through its IRF-association domain (IAD), with the coiled-coil domain (CCD) of STAT2 |
| GO:0005515 protein binding | IPI PMID:24065129 IFNΞ²-dependent increases in STAT1, STAT2, and IRF9 mediate r... | MODIFY | Summary: IPI with STAT2 (P52630), a DNA-binding transcription factor. IRF9 binds STAT2 through its IRF-association domain (IAD) and the STAT2 coiled-coil domain, forming ISGF3. Reason: Generic protein binding is uninformative. The interaction is with a DNA-binding transcription factor and is the structural basis of ISGF3 assembly (PMID:29317535), so DNA-binding transcription factor binding is the informative replacement. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:24065129 The interactions between STAT1 and STAT2 (lanes 2, 3, and 6) and between STAT2 and IRF9 (lanes 6 and 7) were clearly observed in the nuclear fractions PMID:29317535 ISGF3 function depends on selective interaction between IRF9, through its IRF-association domain (IAD), with the coiled-coil domain (CCD) of STAT2 |
| GO:0005515 protein binding | IPI PMID:28514442 Architecture of the human interactome defines protein commun... | REMOVE | Summary: High-throughput interaction screen reporting IRF9 with STAT2 (P52630). The IRF9-STAT2 interaction is real and central to IRF9 function, but generic protein binding is uninformative; the interaction is captured more informatively by the DNA-binding transcription factor binding replacement on the low-throughput STAT2 rows and by the ISGF3 complex annotation. Reason: Generic GO:0005515 from a high-throughput interactome study is uninformative per project protein-binding policy; removal does not dispute the IRF9-STAT2 interaction, which is captured by GO:0140297 and GO:0070721. Supporting Evidence: PMID:29317535 ISGF3 function depends on selective interaction between IRF9, through its IRF-association domain (IAD), with the coiled-coil domain (CCD) of STAT2 |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | REMOVE | Summary: High-throughput interaction screen reporting IRF9 with STAT2 (P52630). The IRF9-STAT2 interaction is real and central to IRF9 function, but generic protein binding is uninformative; the interaction is captured more informatively by the DNA-binding transcription factor binding replacement on the low-throughput STAT2 rows and by the ISGF3 complex annotation. Reason: Generic GO:0005515 from a high-throughput interactome study is uninformative per project protein-binding policy; removal does not dispute the IRF9-STAT2 interaction, which is captured by GO:0140297 and GO:0070721. Supporting Evidence: PMID:29317535 ISGF3 function depends on selective interaction between IRF9, through its IRF-association domain (IAD), with the coiled-coil domain (CCD) of STAT2 |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | REMOVE | Summary: High-throughput interaction screen reporting IRF9 with STAT2 (P52630). The IRF9-STAT2 interaction is real and central to IRF9 function, but generic protein binding is uninformative; the interaction is captured more informatively by the DNA-binding transcription factor binding replacement on the low-throughput STAT2 rows and by the ISGF3 complex annotation. Reason: Generic GO:0005515 from a high-throughput interactome study is uninformative per project protein-binding policy; removal does not dispute the IRF9-STAT2 interaction, which is captured by GO:0140297 and GO:0070721. Supporting Evidence: PMID:29317535 ISGF3 function depends on selective interaction between IRF9, through its IRF-association domain (IAD), with the coiled-coil domain (CCD) of STAT2 |
| GO:0005634 nucleus | EXP PMID:30143481 Life-threatening influenza pneumonitis in a child with inher... | ACCEPT | Summary: Nuclear fractionation of patient and control fibroblasts shows IRF9 in the nucleus, including a basal nuclear pool. Reason: Direct human evidence (PMID:30143481); IRF9 acts in the nucleus on ISREs as part of ISGF3. Supporting Evidence: PMID:30143481 a small amount of IRF9 was visible in the nucleus even under basal conditions PMID:30143481 IRF9 also enables binding of the trimer to DNA, after its translocation to the nucleus |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT (PTN000942746) nucleus location for IRF family transcription factors; human IRF9 is among the donors. Reason: IRF9 is active in the nucleus as the DNA-binding subunit of ISGF3 (PMID:30143481). Supporting Evidence: PMID:30143481 a small amount of IRF9 was visible in the nucleus even under basal conditions PMID:30143481 IRF9 also enables binding of the trimer to DNA, after its translocation to the nucleus |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0191 nucleus). Reason: Matches the curated UniProt localization, which is backed by experimental references. Supporting Evidence: file:human/IRF9/IRF9-uniprot.txt Cytoplasm {ECO:0000269|PubMed:11846981}. Nucleus PMID:30143481 a small amount of IRF9 was visible in the nucleus even under basal conditions |
| GO:0005634 nucleus | TAS PMID:1630447 Subunit of an alpha-interferon-responsive transcription fact... | ACCEPT | Summary: TAS from Veals et al. 1992: activated ISGF3 translocates to the nucleus. Reason: Consistent with experimental nuclear localization (PMID:30143481). Supporting Evidence: PMID:1630447 This receptor-mediated event occurs in the cytoplasm, with subsequent translocation of the activated factor to the nucleus |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-1015699 | ACCEPT | Summary: Reactome places IRF9-containing ISGF3 in the nucleoplasm, where it binds ISRE promoter elements. Reason: Consistent with IRF9 nuclear localization and ISRE binding (PMID:30143481). Supporting Evidence: Reactome:R-HSA-909721 IRF9 is the DNA binding part of this ISGF3 complex PMID:30143481 a small amount of IRF9 was visible in the nucleus even under basal conditions |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-909721 | ACCEPT | Summary: Reactome places IRF9-containing ISGF3 in the nucleoplasm, where it binds ISRE promoter elements. Reason: Consistent with IRF9 nuclear localization and ISRE binding (PMID:30143481). Supporting Evidence: Reactome:R-HSA-909721 IRF9 is the DNA binding part of this ISGF3 complex PMID:30143481 a small amount of IRF9 was visible in the nucleus even under basal conditions |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0086 cytoplasm). Reason: IRF9 resides largely in the cytoplasm until interferon-triggered assembly of ISGF3; curated UniProt localization is experimentally referenced. Supporting Evidence: file:human/IRF9/IRF9-uniprot.txt Cytoplasm {ECO:0000269|PubMed:11846981}. Nucleus PMID:11846981 IRF-3 and IRF-9 are examples of IRFs that are regulated by cellular redistribution |
| GO:0005737 cytoplasm | TAS PMID:1630447 Subunit of an alpha-interferon-responsive transcription fact... | ACCEPT | Summary: TAS from Veals et al. 1992: ISGF3 activation occurs in the cytoplasm. Reason: IRF9 is regulated by nuclear/cytoplasmic redistribution and associates with STAT2 in the cytoplasm (PMID:11846981). Supporting Evidence: PMID:1630447 This receptor-mediated event occurs in the cytoplasm, with subsequent translocation of the activated factor to the nucleus PMID:11846981 IRF-3 and IRF-9 are examples of IRFs that are regulated by cellular redistribution |
| GO:0005829 cytosol | IDA GO_REF:0000052 | ACCEPT | Summary: Human Protein Atlas immunofluorescence localization to the cytosol. Reason: Consistent with the known latent cytoplasmic pool of IRF9 prior to IFN-induced nuclear translocation. Supporting Evidence: PMID:11846981 IRF-3 and IRF-9 are examples of IRFs that are regulated by cellular redistribution PMID:1630447 This receptor-mediated event occurs in the cytoplasm, with subsequent translocation of the activated factor to the nucleus |
| GO:0005829 cytosol | TAS Reactome:R-HSA-1015702 | ACCEPT | Summary: Reactome (Reactome:R-HSA-1015702) depicts IRF9 in the cytosol, where it associates with phosphorylated STAT1:STAT2 to form ISGF3 before nuclear import, or as a newly made ISG product. Reason: IRF9 has a cytoplasmic pool that associates with STAT2 there (PMID:11846981); the location is correct even where the Reactome event is about other ISGF3 subunits. Supporting Evidence: Reactome:R-HSA-909725 The phosphorylated STAT2:STAT1 heterodimer associates with interferon-regulating factor 9 (IRF9) to form the interferon-stimulated gene factor 3 (ISGF3) complex PMID:11846981 IRF-3 and IRF-9 are examples of IRFs that are regulated by cellular redistribution |
| GO:0005829 cytosol | TAS Reactome:R-HSA-1031716 | ACCEPT | Summary: Reactome (Reactome:R-HSA-1031716) depicts IRF9 in the cytosol, where it associates with phosphorylated STAT1:STAT2 to form ISGF3 before nuclear import, or as a newly made ISG product. Reason: IRF9 has a cytoplasmic pool that associates with STAT2 there (PMID:11846981); the location is correct even where the Reactome event is about other ISGF3 subunits. Supporting Evidence: Reactome:R-HSA-909725 The phosphorylated STAT2:STAT1 heterodimer associates with interferon-regulating factor 9 (IRF9) to form the interferon-stimulated gene factor 3 (ISGF3) complex PMID:11846981 IRF-3 and IRF-9 are examples of IRFs that are regulated by cellular redistribution |
| GO:0005829 cytosol | TAS Reactome:R-HSA-909721 | ACCEPT | Summary: Reactome (Reactome:R-HSA-909721) depicts IRF9 in the cytosol, where it associates with phosphorylated STAT1:STAT2 to form ISGF3 before nuclear import, or as a newly made ISG product. Reason: IRF9 has a cytoplasmic pool that associates with STAT2 there (PMID:11846981); the location is correct even where the Reactome event is about other ISGF3 subunits. Supporting Evidence: Reactome:R-HSA-909725 The phosphorylated STAT2:STAT1 heterodimer associates with interferon-regulating factor 9 (IRF9) to form the interferon-stimulated gene factor 3 (ISGF3) complex PMID:11846981 IRF-3 and IRF-9 are examples of IRFs that are regulated by cellular redistribution |
| GO:0005829 cytosol | TAS Reactome:R-HSA-909725 | ACCEPT | Summary: Reactome (Reactome:R-HSA-909725) depicts IRF9 in the cytosol, where it associates with phosphorylated STAT1:STAT2 to form ISGF3 before nuclear import, or as a newly made ISG product. Reason: IRF9 has a cytoplasmic pool that associates with STAT2 there (PMID:11846981); the location is correct even where the Reactome event is about other ISGF3 subunits. Supporting Evidence: Reactome:R-HSA-909725 The phosphorylated STAT2:STAT1 heterodimer associates with interferon-regulating factor 9 (IRF9) to form the interferon-stimulated gene factor 3 (ISGF3) complex PMID:11846981 IRF-3 and IRF-9 are examples of IRFs that are regulated by cellular redistribution |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9710959 | ACCEPT | Summary: Reactome (Reactome:R-HSA-9710959) depicts IRF9 in the cytosol, where it associates with phosphorylated STAT1:STAT2 to form ISGF3 before nuclear import, or as a newly made ISG product. Reason: IRF9 has a cytoplasmic pool that associates with STAT2 there (PMID:11846981); the location is correct even where the Reactome event is about other ISGF3 subunits. Supporting Evidence: Reactome:R-HSA-909725 The phosphorylated STAT2:STAT1 heterodimer associates with interferon-regulating factor 9 (IRF9) to form the interferon-stimulated gene factor 3 (ISGF3) complex PMID:11846981 IRF-3 and IRF-9 are examples of IRFs that are regulated by cellular redistribution |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9710963 | ACCEPT | Summary: Reactome (Reactome:R-HSA-9710963) depicts IRF9 in the cytosol, where it associates with phosphorylated STAT1:STAT2 to form ISGF3 before nuclear import, or as a newly made ISG product. Reason: IRF9 has a cytoplasmic pool that associates with STAT2 there (PMID:11846981); the location is correct even where the Reactome event is about other ISGF3 subunits. Supporting Evidence: Reactome:R-HSA-909725 The phosphorylated STAT2:STAT1 heterodimer associates with interferon-regulating factor 9 (IRF9) to form the interferon-stimulated gene factor 3 (ISGF3) complex PMID:11846981 IRF-3 and IRF-9 are examples of IRFs that are regulated by cellular redistribution |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping to regulation of DNA-templated transcription. Reason: Correct but general; IRF9 positively regulates RNAPII transcription of ISGs, and the gene already carries GO:0045944 (accepted). Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: PMID:30143481 U2A cells transfected with IRF9-Ξex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter PMID:24065129 high expression of Y701F-STAT1, U-STAT2, and IRF9 together in hTERT-HME1 cells significantly increased the expression of the target genes, IFI27, OAS1, OAS2, MX1, IFIT1, and IFIT3 |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | MODIFY | Summary: PAINT (PTN000942746) regulation of transcription by RNAPII across the IRF family; IRF9 is among the donors. Reason: Correct but general. For IRF9 the regulation is positive (activation of ISRE-containing genes), already captured by GO:0045944 on the gene (IDA, PMID:24065129). Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000942746 SUPPORTS TRANSFER IRF-family node; regulation of RNAPII transcription is a sound family-level transfer, and for IRF9 the regulation is positive (ISRE activation). Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: PMID:30143481 U2A cells transfected with IRF9-Ξex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter PMID:24065129 high expression of Y701F-STAT1, U-STAT2, and IRF9 together in hTERT-HME1 cells significantly increased the expression of the target genes, IFI27, OAS1, OAS2, MX1, IFIT1, and IFIT3 |
| GO:0006366 transcription by RNA polymerase II | TAS PMID:1630447 Subunit of an alpha-interferon-responsive transcription fact... | MODIFY | Summary: TAS from Veals et al. 1992 to transcription by RNA polymerase II. Reason: IRF9 does not take part in the core transcription machinery; as a sequence-specific DNA-binding transcription factor subunit it regulates RNAPII transcription positively. Replace with GO:0045944. Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: PMID:1630447 ISGF3 gamma serves as the DNA recognition subunit PMID:30143481 U2A cells transfected with IRF9-Ξex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter |
| GO:0007166 cell surface receptor signaling pathway | TAS PMID:1630447 Subunit of an alpha-interferon-responsive transcription fact... | MODIFY | Summary: TAS from Veals et al. 1992 to the generic cell surface receptor signaling pathway (IFN-alpha receptor signalling). Reason: Correct but general; the specific pathway is type I interferon-mediated signaling, in which IRF9 is the DNA-binding subunit of the effector ISGF3 complex (PMID:30143481). Proposed replacements: type I interferon-mediated signaling pathway Supporting Evidence: PMID:1630447 Recombinant ISGF3 gamma, like the natural protein, interacted with HeLa cell ISGF3 alpha to form the mature ISGF3 DNA-binding complex PMID:30143481 Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-Ξ±2b |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IDA PMID:24065129 IFNΞ²-dependent increases in STAT1, STAT2, and IRF9 mediate r... | ACCEPT | Summary: Cheon et al. 2013: co-expression of STAT1, STAT2 and IRF9 drives expression of ISGs (IFI27, OAS1, OAS2, MX1, IFIT1, IFIT3) via U-ISGF3 bound at ISREs. Reason: Direct human cell evidence for IRF9 acting in ISRE-dependent activation of RNAPII-transcribed genes; corroborated by abolished ISRE reporter activity with patient mutant IRF9 (PMID:30143481). Supporting Evidence: PMID:24065129 high expression of Y701F-STAT1, U-STAT2, and IRF9 together in hTERT-HME1 cells significantly increased the expression of the target genes, IFI27, OAS1, OAS2, MX1, IFIT1, and IFIT3 PMID:24065129 We conclude that the amount of the ternary U-ISGF3 complex is increased in response to high levels of U-STAT1, U-STAT2, and IRF9 without IFN-induced phosphorylation and is present on ISREs in the promoters of U-ISGF3 target genes PMID:30143481 U2A cells transfected with IRF9-Ξex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA electronic annotation to positive regulation of RNAPII transcription. Reason: Consistent with experimental evidence (PMID:24065129, PMID:30143481). Supporting Evidence: PMID:24065129 high expression of Y701F-STAT1, U-STAT2, and IRF9 together in hTERT-HME1 cells significantly increased the expression of the target genes, IFI27, OAS1, OAS2, MX1, IFIT1, and IFIT3 PMID:30143481 U2A cells transfected with IRF9-Ξex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter |
| GO:0070721 ISGF3 complex | IPI PMID:24065129 IFNΞ²-dependent increases in STAT1, STAT2, and IRF9 mediate r... | ACCEPT | Summary: Cheon et al. 2013 co-IP/ChIP shows IRF9 in a ternary STAT1:STAT2:IRF9 (U-ISGF3) complex; classical ISGF3 membership was established when IRF9 was cloned. Reason: IRF9 is the defining DNA-binding subunit of ISGF3 (PMID:1630447); assembly depends on its IAD-STAT2 CCD interface (PMID:29317535); ISGF3 formation is lost in IRF9-deficient patient cells (PMID:30143481). Supporting Evidence: PMID:1630447 Recombinant ISGF3 gamma, like the natural protein, interacted with HeLa cell ISGF3 alpha to form the mature ISGF3 DNA-binding complex PMID:29317535 ISGF3 function depends on selective interaction between IRF9, through its IRF-association domain (IAD), with the coiled-coil domain (CCD) of STAT2 PMID:30143481 Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-Ξ±2b |
| GO:1990837 sequence-specific double-stranded DNA binding | IDA PMID:28473536 Impact of cytosine methylation on DNA binding specificities ... | ACCEPT | Summary: IDA from HT-SELEX profiling of human transcription factors (Yin et al. 2017). IRF9 is not named in the cached main text, so its data are presumably in supplementary tables. Reason: Sequence-specific dsDNA binding is the precise readout of a SELEX assay on naked DNA and is consistent with ISRE binding by IRF9 (PMID:1630447); deferring to the curator who read the supplementary data. Supporting Evidence: PMID:1630447 ISGF3 gamma translated in vitro from recombinant clones bound DNA with a specificity indistinguishable from that of ISGF3 gamma purified from HeLa cells |
| GO:0060337 type I interferon-mediated signaling pathway | IMP PMID:30143481 Life-threatening influenza pneumonitis in a child with inher... | NEW | Summary: IRF9 is the DNA-binding subunit of ISGF3, the effector transcription factor of type I interferon signalling. Patient cells with loss-of-function IRF9 form GAF but not ISGF3 after IFN-alpha2b, lose ISRE binding and ISRE-driven transcription, and are rescued by wild-type IRF9. Reason: IRF9 performs a step of the pathway itself (ISRE recognition by ISGF3), so this is participation, not substrate-like necessity. Comparator check: the two other ISGF3 subunits in the same role, STAT1 (P42224, IDA PMID:23386060) and STAT2 (P52630, IMP), both carry GO:0060337 in GOA; human and mouse IRF9 lack it. Mouse Irf9 knockout cells (same PANTHER subfamily PTHR11949:SF26) likewise lack ISRE binding after IFN stimulation (PMID:9078371). Supporting Evidence: PMID:30143481 Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-Ξ±2b PMID:30143481 Electrophoretic mobility shift assays (EMSAs) confirmed that Pβs cells were not able to form a functional ISGF3 complex following IFN-Ξ±2b stimulation, as evidenced by abolished ISRE binding in vitro PMID:30143481 These phenotypes are rescued by wild-type IRF9, whereas silencing IRF9 expression in control cells increases viral replication PMID:9078371 ISRE-binding activities induced by both IFNs are absent in the p48-negative embryonic fibroblasts (EFs) |
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Download this section (compressed HTML)Q: Should GO:0060337 type I interferon-mediated signaling pathway be annotated to IRF9 in human and mouse, as it is for the other ISGF3 subunits STAT1 and STAT2, or is its absence a deliberate convention?
Q: Does IRF9 contribute to type III (IFN-lambda) and type II (IFN-gamma) responses in human cells to the same extent as reported for mouse p48-deficient cells?
Q: How much of IRF9 function in vivo depends on the acetylation-dependent docking on IFNAR2 reported in a single study, versus STAT2 binding alone?
Experiment: IRF9 ChIP-seq or CUT&RUN in IRF9-deficient patient cells reconstituted with wild-type or IAD-mutant IRF9 after IFN-alpha, IFN-lambda and IFN-gamma, to define the ISGF3- and IRF9-dependent cistrome per interferon type.
Experiment: Test DNA binding and transcriptional activity of IRF9 alone versus in complex with STAT2 (without STAT1) to separate IRF9 DNA recognition from transactivation contributed by STAT2.
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