id: P0DOV2
gene_symbol: Ifi204
product_type: PROTEIN
aliases:
  - p204
  - Ifi-204
  - interferon-inducible protein p204
tags:
  - PYHIN family
  - innate immunity
  - DNA sensor
  - mouse-specific paralog expansion
status: COMPLETE
taxon:
  id: NCBITaxon:10090
  label: Mus musculus
description: >-
  Ifi204 encodes mouse p204, an interferon-inducible PYHIN/HIN-200 family protein with PYD/DAPIN and tandem HIN domains. The literature supports two major functional themes: nucleo-cytoplasmic transcriptional/differentiation control through interactions with UBF1, Runx2/Cbfa1, Id proteins, and signaling regulators, and context-dependent innate immune DNA-sensor activity linked to interferon and bacterial/viral challenge. Falcon synthesis emphasizes that the strongest classic evidence is for transcriptional coregulation, nucleolar/nuclear localization, and differentiation/proliferation control, while recent DNA-sensor and antiviral roles are real but experimentally context-dependent.
references:
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with GO terms
    findings: []
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings: []
  - id: GO_REF:0000044
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
    findings: []
  - id: GO_REF:0000119
    title: Automated transfer of experimentally-verified manual GO annotation data to mouse-human orthologs
    findings: []
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods
    findings: []
  - id: PMID:2477366
    title: Interferons as gene activators. Indications for repeated gene duplication during the evolution of a cluster of interferon-activatable genes on murine chromosome 1.
    findings:
      - statement: >-
          The Ifi204 gene lies within a cluster of interferon-activatable genes on murine
          chromosome 1 that arose by repeated gene duplication. The 202 and 204 gene products
          share conserved 200-amino acid segments and similar regulatory regions with
          interferon-responsive enhancers.
        supporting_text: >-
          sequences of three genes from the cluster (the 201, 202, and 204 genes) are very
          similar in a segment extending from at least 550 nucleotides upstream of the 3'
          end of the transcription initiation region to beyond the first exon intron border
          (96% similarity between the 202 and 204 genes and 89% similarity between the 201
          and 204 genes)
  - id: PMID:10329630
    title: The interferon-inducible nucleolar p204 protein binds the ribosomal RNA-specific UBF1 transcription factor and inhibits ribosomal RNA transcription.
    findings:
      - statement: >-
          p204 is primarily nucleolar and inhibits rRNA transcription by binding UBF1.
          Interferon treatment induces p204 and retards cell proliferation via inhibition
          of rRNA transcription.
        supporting_text: >-
          p204, a member of the interferon-inducible p200 family of murine proteins, is
          primarily nucleolar...This induction resulted in retardation of cell
          proliferation and inhibition of rRNA transcription in vivo...A direct interaction
          between p204 and UBF1 was revealed in vitro in pull-down assays, and in vivo by
          co-immunoprecipitation from cell extracts
  - id: PMID:11940648
    title: The MyoD-inducible p204 protein overcomes the inhibition of myoblast differentiation by Id proteins.
    findings:
      - statement: >-
          p204 is required for C2C12 myoblast differentiation. It binds Id1, Id2, and Id3,
          overcomes their inhibition of MyoD/E47-dependent transcription, and promotes their
          ubiquitination and degradation. p204 is phosphorylated and translocated from
          nucleus to cytoplasm during myoblast fusion.
        supporting_text: >-
          p204 is required for the differentiation of C2C12 myoblasts...it enables the
          differentiation, at least in part, by overcoming the inhibition of the activities
          of the MyoD and E47 proteins by the Id proteins: Id1, Id2, and Id3...p204 bound
          to the Id proteins in vitro and in vivo
  - id: PMID:12513910
    title: The mouse interferon-inducible gene Ifi204 product interacts with the Tpr protein, a component of the nuclear pore complex.
    findings:
      - statement: >-
          p204 interacts with the Tpr protein (nucleoporin) in yeast two-hybrid and
          coimmunoprecipitation experiments. Tpr mediates p204 translocation from cytoplasm
          to nucleus following IFN treatment. p204 localizes to nucleolus and nuclear
          inclusion bodies.
        supporting_text: >-
          We have used yeast two-hybrid screening to isolate cDNA-encoding proteins
          interacting with the protein encoded by the interferon (IFN)-inducible gene
          Ifi204...in vivo interaction was demonstrated by coimmunoprecipitation
          experiments...it appears to mediate p204 translocation from the cytoplasmic to
          the nuclear compartment following IFN treatment
  - id: PMID:14654789
    title: A member of the Pyrin family, IFI16, is a novel BRCA1-associated protein involved in the p53-mediated apoptosis pathway.
    findings:
      - statement: >-
          Human IFI16 interacts with BRCA1 via its Pyrin domain and participates in
          p53-mediated apoptosis. IFI16 localizes to nucleoplasm and nucleoli. This paper
          is about human IFI16, and ISO annotations to mouse Ifi204 are based on orthology
          transfer.
        supporting_text: >-
          IFI16 contains the Pyrin/PAAD/DAPIN domain, commonly found in cell
          death-associated proteins. BRCA1 (aa 502-802) interacted with the IFI16 Pyrin
          domain (aa 1-130). We found that IFI16 was localized in the nucleoplasm and
          nucleoli
  - id: PMID:15557274
    title: The interferon-inducible p204 protein acts as a transcriptional coactivator of Cbfa1 and enhances osteoblast differentiation.
    findings:
      - statement: >-
          p204 acts as a transcriptional coactivator of Cbfa1/Runx2 during osteoblast
          differentiation. It is expressed in embryonic osteoblasts and hypertrophic
          chondrocytes. Both HIN domains bind Runx2. Overexpression enhances BMP-2-induced
          osteoblast differentiation with elevated alkaline phosphatase and osteocalcin.
        supporting_text: >-
          p204 is expressed in embryonic osteoblasts and hypertrophic chondrocytes in the
          growth plate as well as in the calvaria osteoblasts of neonatal mice...
          Overexpression of p204 enhances the BMP-2-induced osteoblast differentiation
          in vitro, as revealed by elevated alkaline phosphatase activity and osteocalcin
          production. p204 acts as a cofactor of Cbfa1
  - id: PMID:16244109
    title: The interferon-inducible gene, Ifi204, is transcriptionally activated in response to M-CSF, and its expression favors macrophage differentiation in myeloid progenitor cells.
    findings:
      - statement: >-
          Ifi204 is activated by M-CSF and promotes macrophage differentiation. Enforced
          expression decreases proliferation and favors macrophage differentiation of
          FD-Fms cells.
        supporting_text: >-
          Ifi204 was transcriptionally activated in response to M-CSF...enforced
          expression of Ifi204 strongly decreased IL-3- and M-CSF-dependent proliferation
          and conversely, favored macrophage differentiation of FD-Fms cells in response
          to M-CSF
  - id: PMID:16556595
    title: p204 is required for the differentiation of P19 murine embryonal carcinoma cells to beating cardiac myocytes.
    findings:
      - statement: >-
          p204 is required for cardiac myocyte differentiation. Expression is synergistically
          activated by cardiac transcription factors Gata4, Nkx2.5, and Tbx5. Contains a
          nuclear export signal required for cytoplasmic translocation during differentiation.
        supporting_text: >-
          p204 was also required for the differentiation of cultured P19 murine embryonal
          carcinoma stem cells to beating cardiac myocytes...p204 expression was
          synergistically transactivated by the cardiac Gata4, Nkx2.5, and Tbx5
          transcription factors...p204 contains a nuclear export signal and was partially
          translocated to the cytoplasm during the differentiation
  - id: PMID:19158679
    title: An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome.
    findings:
      - statement: >-
          This paper primarily identifies AIM2 as a cytoplasmic DNA sensor for the
          inflammasome. AIM2 binds dsDNA via its HIN domain and recruits ASC. The paper is
          not primarily about Ifi204/p204. ISO annotations to Ifi204 from this reference are
          based on orthology transfer from human IFI16.
        supporting_text: >-
          AIM2 showed specificity for double-stranded DNA. It also recruited the
          inflammasome adaptor ASC and localized to ASC 'speckles'...AIM2 was sufficient
          for inflammasome activation
  - id: PMID:21795542
    title: Developmental profiling of spiral ganglion neurons reveals insights into auditory circuit assembly.
    findings:
      - statement: >-
          Transcriptomic profiling study of spiral ganglion neurons. Ifi204 is one of many
          genes with altered expression during auditory development. The study does not
          functionally characterize Ifi204 in inner ear development.
        supporting_text: >-
          We catalogued gene expression in mouse SG neurons from embryonic day 12, when
          SG neurons first extend projections, up until postnatal day 15, after the onset
          of hearing...exhibit a dramatic increase in immune gene expression
  - id: PMID:22871040
    title: The mammalian PYHIN gene family - phylogeny, evolution and expression.
    findings:
      - statement: >-
          The mouse PYHIN family has 14 members (vs 4 in human), all arising by
          lineage-specific duplication on chromosome 1. Only AIM2 has clear orthology
          across species. The other mouse genes, including Ifi204, arose by duplication
          and rearrangement within the mouse lineage.
        supporting_text: >-
          Placental mammals show variable family expansions, from one gene in cow to four
          in human and 14 in mouse...The other 13 mouse genes have arisen by duplication
          and rearrangement within the lineage
  - id: PMID:23012479
    title: Impact of lactobacilli on orally acquired listeriosis.
    findings:
      - statement: >-
          Ifi204 is one of many interferon-stimulated genes whose expression is affected
          by lactobacilli treatment during Listeria infection. The paper does not
          functionally characterize Ifi204 in bacterial response.
        supporting_text: >-
          A whole genome intestinal transcriptomic analysis revealed that each
          Lactobacillus changes expression of a specific subset of genes during
          infection, with IFN-stimulated genes (ISGs) being the most affected by both
          lactobacilli
  - id: PMID:25710914
    title: cGAS and Ifi204 cooperate to produce type I IFNs in response to Francisella infection.
    findings:
      - statement: >-
          cGAS and Ifi204 are both required for the STING-dependent type I IFN response to
          Francisella novicida in murine macrophages. CRISPR knockouts of cGAS, Ifi204, and
          Sting in RAW264.7 cells demonstrate cooperation between cGAS and Ifi204 in dsDNA
          sensing.
        supporting_text: >-
          the cytosolic DNA sensors, cyclic GMP-AMP synthase (cGAS) and Ifi204, are both
          required for the STING-dependent type I IFN response to F. novicida infection in
          both primary and immortalized murine macrophages
  - id: PMID:28529930
    title: "The Central Role of IFI204 in IFN-β Release and Autophagy Activation during Mycobacterium bovis Infection."
    findings:
      - statement: >-
          IFI204 is acetylated upon M. bovis infection, translocates from nucleus to
          cytoplasm, and recruits STING to activate TBK1-IRF3 signaling and IFN-beta
          production. Knockdown blocks IFN-beta production and autophagy marker LC3
          expression.
        supporting_text: >-
          Knockdown of the IFI204 in immortalized and primary murine macrophages blocked
          IFN-beta production and autophagy marker LC3 expression
  - id: PMID:30936875
    title: DNA Sensor IFI204 Contributes to Host Defense Against Staphylococcus aureus Infection in Mice.
    findings:
      - statement: >-
          IFI204-deficient mice show increased susceptibility to S. aureus pulmonary
          infection with decreased inflammatory cytokines, impaired STING-IRF3 and NF-kB
          pathways, and defective extracellular trap formation in macrophages and
          neutrophils.
        supporting_text: >-
          IFI204 deficiency results in decreased survival, increased bacterial loads,
          severe organs damage, and decreased recruitment of neutrophils and macrophages
  - id: PMID:33619523
    title: Structural mechanism of DNA recognition by the p204 HIN domain.
    findings:
      - statement: >-
          Crystal structures of p204 HINa, HINb, and HINab:dsDNA complex reveal
          non-sequence-specific dsDNA binding via alpha-2 helices and linker region.
          Both HINa and HINb are required for dsDNA recognition. HINa dimerization
          interface is involved in DNA binding.
        supporting_text: >-
          p204 HINab binds dsDNA mainly through alpha2 helix of HINa and HINb, and the
          linker between them...Both HINa and HINb are vital for HINab recognition of
          dsDNA, as confirmed by fluorescence polarization assays
  - id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
    title: Falcon deep research report on mouse Ifi204 function
    findings: []
existing_annotations:
  - term:
      id: GO:0003690
      label: double-stranded DNA binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        Core molecular function of Ifi204. The tandem HIN-200 OB-fold domains bind
        dsDNA in a non-sequence-specific manner, confirmed by crystal structures of
        the HINab:DNA complex and fluorescence polarization assays.
      action: ACCEPT
      reason: >-
        dsDNA binding is the central biochemical activity of Ifi204 HIN domains,
        directly demonstrated by structural and biochemical studies.
      supported_by:
        - reference_id: PMID:33619523
          supporting_text: >-
            p204 HINab binds dsDNA mainly through alpha2 helix of HINa and HINb, and
            the linker between them, revealing a similar HIN:DNA binding mode
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-bioreason-sft.md
          supporting_text: >-
            The tandem OB-fold HIN region binds duplex DNA directly, supporting
            GO:0003690 double-stranded DNA binding
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005730
      label: nucleolus
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        Well-supported localization. p204 is primarily nucleolar in proliferating
        cells, confirmed by immunofluorescence.
      action: ACCEPT
      reason: >-
        Nucleolar localization is directly demonstrated by immunofluorescence in
        multiple studies, and p204 inhibits rRNA transcription through nucleolar
        interaction with UBF1.
      supported_by:
        - reference_id: PMID:10329630
          supporting_text: >-
            p204, a member of the interferon-inducible p200 family of murine proteins,
            is primarily nucleolar
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0035458
      label: cellular response to interferon-beta
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        The supporting evidence establishes Ifi204 as a DNA sensor that promotes
        type I IFN/IFN-beta production, not specifically as a gene product responding
        to IFN-beta stimulation.
      action: MODIFY
      reason: >-
        Replace the response-to-IFN-beta term with production/regulation terms that
        match the accessible Ifi204 evidence from Francisella and mycobacterial
        infection models.
      proposed_replacement_terms:
        - id: GO:0032728
          label: positive regulation of interferon-beta production
        - id: GO:0032481
          label: positive regulation of type I interferon production
      supported_by:
        - reference_id: PMID:25710914
          supporting_text: >-
            cGAS and Ifi204 cooperate to sense cytosolic dsDNA and F. novicida
            infection to produce a strong type I IFN response
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0002218
      label: activation of innate immune response
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        Core biological process. Ifi204 senses cytosolic dsDNA and activates the
        STING-TBK1-IRF3 innate immune signaling pathway. KO mice show impaired
        innate immune responses to bacterial infection.
      action: ACCEPT
      reason: >-
        Multiple studies demonstrate Ifi204 is required for innate immune activation
        via the STING pathway in response to bacterial DNA.
      supported_by:
        - reference_id: PMID:30936875
          supporting_text: >-
            IFI204 deficiency results in decreased survival, increased bacterial loads,
            severe organs damage, and decreased recruitment of neutrophils and macrophages
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005654
      label: nucleoplasm
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        Ifi204 is nuclear in proliferating cells, present in nucleoplasm as well as
        nucleolus and nuclear bodies.
      action: ACCEPT
      reason: >-
        Nuclear/nucleoplasmic localization is well-documented by immunofluorescence
        and consistent with its transcriptional regulatory roles.
      supported_by:
        - reference_id: PMID:12513910
          supporting_text: >-
            When superimposed on optical sections obtained with anti-p204 Abs, these
            colocalized, with the sole exception of the nucleolar compartment stained
            by the anti-p204 Abs only
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        Ifi204 translocates to the cytosol during differentiation and upon bacterial
        infection, where it functions as a DNA sensor cooperating with cGAS to
        activate the STING pathway.
      action: ACCEPT
      reason: >-
        Cytosolic localization is well-documented during infection (after acetylation)
        and during differentiation, and is functionally important for DNA sensing.
      supported_by:
        - reference_id: PMID:28529930
          supporting_text: >-
            IFI204 first undergoes acetylation and then translocates from nucleus into
            cytoplasm to recruit STING for activation of TBK1-dependent IRF3 nuclear
            translocation
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0002218
      label: activation of innate immune response
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: >-
        Redundant with the IBA annotation for the same term. The InterPro-based
        annotation from the HIN-200 family domain is consistent with experimental
        evidence.
      action: ACCEPT
      reason: >-
        Correct annotation from InterPro HIN-200 family classification, supported
        by extensive experimental evidence for innate immune activation.
      supported_by:
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: >-
        Ifi204 is nuclear in proliferating cells, consistent with UniProt subcellular
        location annotation.
      action: ACCEPT
      reason: >-
        Nuclear localization is well-established by multiple experimental studies.
      supported_by:
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005730
      label: nucleolus
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: >-
        Redundant with IBA and IDA annotations for the same term. Consistent with
        experimental evidence.
      action: ACCEPT
      reason: Correct annotation supported by direct experimental evidence.
      supported_by:
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005737
      label: cytoplasm
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: >-
        Ifi204 translocates to cytoplasm during differentiation and infection.
        This annotation is more general than cytosol but still correct.
      action: ACCEPT
      reason: >-
        Cytoplasmic localization is well-documented during differentiation and
        bacterial infection.
      supported_by:
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0035458
      label: cellular response to interferon-beta
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >-
        Redundant with the IBA response-to-IFN-beta annotation, but the available
        Ifi204 evidence supports type I IFN/IFN-beta production rather than cellular
        response to IFN-beta.
      action: MODIFY
      reason: Replace with production/regulation terms that capture Ifi204-dependent
        activation of the STING/type I interferon response.
      proposed_replacement_terms:
        - id: GO:0032728
          label: positive regulation of interferon-beta production
        - id: GO:0032481
          label: positive regulation of type I interferon production
      supported_by:
        - reference_id: PMID:25710914
          supporting_text: >-
            cGAS and Ifi204 cooperate to sense cytosolic dsDNA and F. novicida
            infection to produce a strong type I IFN response
  - term:
      id: GO:0005654
      label: nucleoplasm
    evidence_type: ISO
    original_reference_id: GO_REF:0000119
    review:
      summary: >-
        ISO transfer from human IFI16. Nucleoplasmic localization is confirmed
        by direct studies of Ifi204.
      action: ACCEPT
      reason: Consistent with direct experimental evidence for Ifi204 nuclear localization.
      supported_by:
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005730
      label: nucleolus
    evidence_type: ISO
    original_reference_id: GO_REF:0000119
    review:
      summary: >-
        ISO transfer from human IFI16. Nucleolar localization is directly
        demonstrated for Ifi204.
      action: ACCEPT
      reason: Redundant with IDA evidence but correct.
      supported_by:
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: ISO
    original_reference_id: GO_REF:0000119
    review:
      summary: >-
        ISO transfer from human IFI16. Cytosolic localization during infection
        is directly demonstrated for Ifi204.
      action: ACCEPT
      reason: Consistent with direct experimental evidence.
      supported_by:
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0031625
      label: ubiquitin protein ligase binding
    evidence_type: ISO
    original_reference_id: GO_REF:0000119
    review:
      summary: >-
        ISO transfer from human ortholog. While p204 promotes ubiquitination
        and degradation of Id proteins, this appears to be indirect (p204
        sequesters Id proteins and promotes their ubiquitination by other ligases
        rather than directly binding ubiquitin ligases). Evidence is limited for
        direct ubiquitin ligase binding.
      action: KEEP_AS_NON_CORE
      reason: >-
        The ISO transfer is plausible but the direct evidence for p204 binding
        ubiquitin ligases is limited. The ubiquitination of Id proteins promoted
        by p204 may be indirect.
      supported_by:
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0032991
      label: protein-containing complex
    evidence_type: ISO
    original_reference_id: GO_REF:0000119
    review:
      summary: >-
        Generic complex annotation. Ifi204 forms complexes with multiple partners
        including UBF1, Runx2, Id proteins, Tpr, and STING, but this term is too
        vague to be informative.
      action: KEEP_AS_NON_CORE
      reason: >-
        While Ifi204 participates in multiple protein complexes, the term
        protein-containing complex is too generic to be useful. More specific
        complex annotations would be preferable.
      supported_by:
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0009617
      label: response to bacterium
    evidence_type: IEP
    original_reference_id: PMID:23012479
    review:
      summary: >-
        Based on expression change during Listeria infection in a lactobacilli
        study. Ifi204 is one of many ISGs affected. While the annotation is not
        wrong (Ifi204 does respond to bacterial infection), this specific paper
        provides only weak expression evidence.
      action: MODIFY
      reason: >-
        While expression-based evidence from PMID:23012479 is weak, much stronger
        evidence from PMID:30936875 (IFI204-KO mice with S. aureus) and
        PMID:25710914 (Francisella response) directly demonstrates a role in
        defense response to bacterium, which is more specific and appropriate.
      proposed_replacement_terms:
        - id: GO:0042742
          label: defense response to bacterium
      supported_by:
        - reference_id: PMID:23012479
          supporting_text: >-
            IFN-stimulated genes (ISGs) being the most affected by both lactobacilli
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
      additional_reference_ids:
        - PMID:30936875
        - PMID:25710914
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:12513910
    review:
      summary: >-
        Based on interaction with Tpr (nucleoporin). Per curation guidelines,
        protein binding is too generic and should be replaced with a more
        informative MF term. The interaction with Tpr is relevant to
        nuclear-cytoplasmic transport of p204.
      action: REMOVE
      reason: >-
        Per curation guidelines, GO:0005515 protein binding is uninformative.
        The Tpr interaction is better captured by noting Tpr as a transport
        partner rather than a generic protein binding annotation.
      supported_by:
        - reference_id: PMID:12513910
          supporting_text: >-
            in vivo interaction was demonstrated by coimmunoprecipitation experiments
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005730
      label: nucleolus
    evidence_type: IDA
    original_reference_id: PMID:12513910
    review:
      summary: >-
        Direct demonstration of nucleolar localization by immunofluorescence.
        Anti-p204 antibodies stained the nucleolar compartment.
      action: ACCEPT
      reason: >-
        Direct experimental evidence for nucleolar localization, consistent
        with p204's function in inhibiting rRNA transcription.
      supported_by:
        - reference_id: PMID:12513910
          supporting_text: >-
            the sole exception of the nucleolar compartment stained by the
            anti-p204 Abs only
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0035457
      label: cellular response to interferon-alpha
    evidence_type: IDA
    original_reference_id: PMID:12513910
    review:
      summary: >-
        p204 expression is induced by interferon treatment. The study shows
        p204 translocates to the nucleus after IFN treatment, mediated by
        Tpr interaction.
      action: ACCEPT
      reason: >-
        Direct evidence that Ifi204 responds to interferon treatment with
        nuclear translocation mediated by Tpr.
      supported_by:
        - reference_id: PMID:12513910
          supporting_text: >-
            Although the specific function of Tpr is not defined, it appears to
            mediate p204 translocation from the cytoplasmic to the nuclear
            compartment following IFN treatment
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0042405
      label: nuclear inclusion body
    evidence_type: IDA
    original_reference_id: PMID:12513910
    review:
      summary: >-
        p204 localizes to discrete nuclear foci/inclusion bodies as shown
        by immunofluorescence, colocalizing with Tpr in the nuclear interior.
      action: ACCEPT
      reason: Direct immunofluorescence evidence for localization to nuclear inclusion bodies.
      supported_by:
        - reference_id: PMID:12513910
          supporting_text: >-
            The intranuclear Tpr occurred in apparently discrete foci. When
            superimposed on optical sections obtained with anti-p204 Abs, these
            colocalized
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0048839
      label: inner ear development
    evidence_type: IDA
    original_reference_id: PMID:21795542
    review:
      summary: >-
        Based on transcriptomic profiling of spiral ganglion neurons. Ifi204
        is one of many genes with altered expression during auditory development.
        The paper is a large-scale profiling study, not a functional study of
        Ifi204. Expression in a developing tissue does not demonstrate functional
        involvement.
      action: MARK_AS_OVER_ANNOTATED
      reason: >-
        This annotation is based solely on expression profiling data from a
        transcriptomics screen. There is no functional evidence (knockdown,
        knockout, or other perturbation) that Ifi204 plays a role in inner ear
        development. The expression change likely reflects the interferon-responsive
        nature of Ifi204 during immune gene upregulation in maturing neurons,
        not a specific developmental function.
      supported_by:
        - reference_id: PMID:21795542
          supporting_text: >-
            We catalogued gene expression in mouse SG neurons from embryonic day 12
            ...exhibit a dramatic increase in immune gene expression
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: ISO
    original_reference_id: PMID:19158679
    review:
      summary: >-
        ISO transfer from human IFI16 based on an AIM2-focused paper is weak, but
        nuclear localization itself is supported by direct p204/Ifi204 localization
        evidence.
      action: ACCEPT
      reason: >-
        Nuclear localization is well-established for Ifi204 by direct studies,
        making this ISO annotation consistent with known biology.
      supported_by:
        - reference_id: PMID:12513910
          supporting_text: >-
            When superimposed on optical sections obtained with anti-p204 Abs,
            these colocalized, with the sole exception of the nucleolar compartment
            stained by the anti-p204 Abs only
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0016607
      label: nuclear speck
    evidence_type: ISO
    original_reference_id: PMID:19158679
    review:
      summary: >-
        The cited AIM2 paper describes cytoplasmic ASC inflammasome speckles, not
        nuclear speckles, and direct Ifi204 evidence supports p204/Tpr intranuclear
        foci and nucleolus rather than GO nuclear speck.
      action: REMOVE
      reason: >-
        The ISO transfer is not adequately supported for this specific cellular
        component. ASC speckles are inflammasome structures, and p204 intranuclear
        foci should not be equated with nuclear speckles without direct evidence.
      supported_by:
        - reference_id: PMID:19158679
          supporting_text: >-
            AIM2 showed specificity for double-stranded DNA. It also recruited
            the inflammasome adaptor ASC and localized to ASC 'speckles'
        - reference_id: PMID:12513910
          supporting_text: >-
            The intranuclear Tpr occurred in apparently discrete foci
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0003690
      label: double-stranded DNA binding
    evidence_type: IDA
    original_reference_id: PMID:19158679
    review:
      summary: >-
        While PMID:19158679 is primarily about AIM2, dsDNA binding by Ifi204/p204
        is directly supported by structural and biochemical studies of p204 HIN
        domains.
      action: ACCEPT
      reason: >-
        dsDNA binding is the core molecular function of Ifi204 HIN domains,
        extensively validated by crystal structures and biochemical assays.
      supported_by:
        - reference_id: PMID:33619523
          supporting_text: >-
            p204 HINab binds dsDNA mainly through α2 helix of HINa and HINb, and
            the linker between them, revealing a similar HIN:DNA binding mode
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
      additional_reference_ids:
        - PMID:33619523
  - term:
      id: GO:0035458
      label: cellular response to interferon-beta
    evidence_type: IDA
    original_reference_id: PMID:19158679
    review:
      summary: >-
        PMID:19158679 is AIM2-focused and does not support Ifi204 cellular response
        to IFN-beta. Ifi204 evidence instead supports DNA-sensor-dependent
        IFN-beta/type I interferon production.
      action: MODIFY
      reason: >-
        Replace this term with production/regulation terms matching the direct
        Ifi204 evidence. The accessible studies show Ifi204 is required for
        STING-dependent type I IFN or IFN-beta production after bacterial DNA
        sensing, not simply response to IFN-beta.
      proposed_replacement_terms:
        - id: GO:0032728
          label: positive regulation of interferon-beta production
        - id: GO:0032481
          label: positive regulation of type I interferon production
      supported_by:
        - reference_id: PMID:25710914
          supporting_text: >-
            cGAS and Ifi204 cooperate to sense cytosolic dsDNA and F. novicida
            infection to produce a strong type I IFN response
        - reference_id: PMID:28529930
          supporting_text: >-
            IFI204 plays an important role in IFN-β release during M. bovis
            infection in murine macrophage model
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
      additional_reference_ids:
        - PMID:25710914
        - PMID:28529930
  - term:
      id: GO:0003712
      label: transcription coregulator activity
    evidence_type: IGI
    original_reference_id: PMID:15557274
    review:
      summary: >-
        p204 acts as a transcriptional coactivator of Cbfa1/Runx2 during
        osteoblast differentiation. High p204 levels augment Runx2-dependent
        transcription; low levels decrease it. p204 associates with Runx2
        both in vitro and in vivo.
      action: ACCEPT
      reason: >-
        Core molecular function demonstrated by direct biochemical evidence.
        p204 enhances Runx2-dependent transcription as a coactivator.
      supported_by:
        - reference_id: PMID:15557274
          supporting_text: >-
            high levels of p204 augment, whereas the lowering of p204 level
            decreases, the Cbfa1-dependent transcription, and...p204 associates
            with Cbfa1 both in vitro and in vivo
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:15557274
    review:
      summary: >-
        Based on interaction with Runx2/Cbfa1. Per curation guidelines, protein
        binding is too generic. The interaction with Runx2 is better captured by
        the transcription coregulator activity annotation.
      action: REMOVE
      reason: >-
        Per curation guidelines, GO:0005515 protein binding is uninformative.
        The functionally relevant interaction is captured by GO:0003712
        transcription coregulator activity.
      supported_by:
        - reference_id: PMID:15557274
          supporting_text: >-
            p204 associates with Cbfa1 both in vitro and in vivo. Two nonoverlapping
            segments in p204 bind to Cbfa1
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0006357
      label: regulation of transcription by RNA polymerase II
    evidence_type: IDA
    original_reference_id: PMID:15557274
    review:
      summary: >-
        p204 modulates Runx2-dependent transcription from RNA Pol II promoters
        during osteoblast differentiation. Also shown to regulate transcription
        of rRNA (via UBF1) and other target genes.
      action: ACCEPT
      reason: >-
        Direct evidence for regulation of Pol II transcription through
        coactivation of Runx2 and modulation of other transcription factors.
      supported_by:
        - reference_id: PMID:15557274
          supporting_text: >-
            p204 acts as a cofactor of Cbfa1...high levels of p204 augment...the
            Cbfa1-dependent transcription
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0045669
      label: positive regulation of osteoblast differentiation
    evidence_type: IGI
    original_reference_id: PMID:15557274
    review:
      summary: >-
        p204 overexpression enhances BMP-2-induced osteoblast differentiation
        in vitro, with elevated alkaline phosphatase activity and osteocalcin
        production. Expressed in embryonic osteoblasts and growth plate
        chondrocytes.
      action: KEEP_AS_NON_CORE
      reason: >-
        Valid annotation but represents a non-core, context-dependent function.
        Osteoblast differentiation is one of several differentiation programs
        p204 participates in (also myoblast and cardiac), reflecting its general
        role in overcoming Id protein inhibition rather than a specific osteoblast
        function.
      supported_by:
        - reference_id: PMID:15557274
          supporting_text: >-
            Overexpression of p204 enhances the BMP-2-induced osteoblast
            differentiation in vitro, as revealed by elevated alkaline phosphatase
            activity and osteocalcin production
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005654
      label: nucleoplasm
    evidence_type: ISO
    original_reference_id: PMID:14654789
    review:
      summary: >-
        ISO from human IFI16. Nucleoplasmic localization of IFI16 is demonstrated
        by immunofluorescence. Consistent with direct evidence for Ifi204.
      action: ACCEPT
      reason: Consistent with direct experimental evidence for Ifi204.
      supported_by:
        - reference_id: PMID:14654789
          supporting_text: >-
            We found that IFI16 was localized in the nucleoplasm and nucleoli
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0005730
      label: nucleolus
    evidence_type: ISO
    original_reference_id: PMID:14654789
    review:
      summary: >-
        ISO from human IFI16. IFI16 nucleolar localization is demonstrated.
        Consistent with direct evidence for Ifi204.
      action: ACCEPT
      reason: Redundant with IDA evidence but correct.
      supported_by:
        - reference_id: PMID:14654789
          supporting_text: >-
            We found that IFI16 was localized in the nucleoplasm and nucleoli
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
  - term:
      id: GO:0042771
      label: intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
    evidence_type: ISO
    original_reference_id: PMID:14654789
    review:
      summary: >-
        ISO from human IFI16. PMID:14654789 shows IFI16 interacts with BRCA1
        and collaborates in p53-mediated apoptosis after DNA damage. p204 is
        known to inhibit cell growth via p53-dependent pathways, but direct
        evidence for p53-mediated apoptotic signaling in response to DNA damage
        is limited for mouse Ifi204 specifically.
      action: KEEP_AS_NON_CORE
      reason: >-
        The ISO transfer from IFI16 is plausible given that p204 also interacts
        with p53 and modulates cell growth. However, the specific apoptotic
        signaling pathway in response to DNA damage has not been directly
        demonstrated for mouse Ifi204. Keep as non-core pending direct evidence.
      supported_by:
        - reference_id: PMID:14654789
          supporting_text: >-
            Coexpression of IFI16 and BRCA1 enhanced DNA damage-induced apoptosis
            in mouse embryonic fibroblasts from BRCA1 mutant mice expressing
            wild-type p53
        - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
          supporting_text: '[Falcon deep-research synthesis used for this annotation decision.]'
core_functions:
  - description: >-
      Nuclear transcriptional coregulator that modulates gene expression during
      cell differentiation. Acts as a coactivator of Runx2/Cbfa1 during
      osteoblast differentiation, and also inhibits rRNA transcription by binding
      UBF1. Promotes multiple differentiation programs (skeletal muscle, cardiac
      myocyte, macrophage) by sequestering and degrading Id inhibitor proteins.
    molecular_function:
      id: GO:0003712
      label: transcription coregulator activity
    directly_involved_in:
      - id: GO:0006357
        label: regulation of transcription by RNA polymerase II
    locations:
      - id: GO:0005730
        label: nucleolus
      - id: GO:0005654
        label: nucleoplasm
    supported_by:
      - reference_id: PMID:15557274
        supporting_text: >-
          p204 acts as a cofactor of Cbfa1...p204 associates with Cbfa1
          both in vitro and in vivo
      - reference_id: PMID:10329630
        supporting_text: >-
          p204...inhibits ribosomal RNA transcription...inhibition was overcome
          by addition of UBF1
      - reference_id: PMID:11940648
        supporting_text: >-
          p204 bound to the Id proteins in vitro and in vivo...Addition of p204
          overcame the inhibition by the Id proteins of the binding of MyoD and
          E47 to DNA
      - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
        supporting_text: '[Falcon synthesis supports Ifi204/p204 as a PYHIN protein with transcriptional coregulator, differentiation-control, nucleolar, and context-dependent DNA-sensor roles.]'
  - description: >-
      Cytosolic DNA sensor that cooperates with cGAS to detect foreign dsDNA and
      activate the STING-TBK1-IRF3 signaling pathway for type I interferon
      production. Upon bacterial infection, becomes acetylated and translocates
      from nucleus to cytoplasm where it recruits STING. Essential for host
      defense against bacterial pathogens.
    molecular_function:
      id: GO:0003690
      label: double-stranded DNA binding
    directly_involved_in:
      - id: GO:0002218
        label: activation of innate immune response
      - id: GO:0032481
        label: positive regulation of type I interferon production
      - id: GO:0042742
        label: defense response to bacterium
    locations:
      - id: GO:0005829
        label: cytosol
    supported_by:
      - reference_id: PMID:25710914
        supporting_text: >-
          cGAS and Ifi204 cooperate to sense dsDNA and activate the
          STING-dependent type I IFN pathway
      - reference_id: PMID:30936875
        supporting_text: >-
          IFI204 deficiency results in decreased survival, increased bacterial
          loads, severe organs damage
      - reference_id: PMID:28529930
        supporting_text: >-
          IFI204 first undergoes acetylation and then translocates from nucleus
          into cytoplasm to recruit STING
      - reference_id: file:mouse/Ifi204/Ifi204-deep-research-falcon.md
        supporting_text: '[Falcon synthesis supports Ifi204/p204 as a PYHIN protein with transcriptional coregulator, differentiation-control, nucleolar, and context-dependent DNA-sensor roles.]'
suggested_questions:
  - question: >-
      What is the relative contribution of Ifi204 vs cGAS in cytosolic DNA
      sensing? Does Ifi204 have a non-redundant function distinct from cGAS
      in the STING pathway?
    experts:
      - Denise M. Monack
  - question: >-
      Given the mouse-specific paralog expansion of PYHIN genes (14 in mouse
      vs 4 in human), is there functional subfunctionalization among the
      mouse PYHIN paralogs? Do other mouse PYHIN proteins compensate when
      Ifi204 is deleted?
    experts:
      - Katryn J. Stacey
  - question: >-
      Is the role of Ifi204 in cell differentiation (osteoblast, myocyte,
      macrophage) dependent on its DNA-binding HIN domains, its PYRIN domain,
      or both? Are these differentiation functions shared with human IFI16?
    experts:
      - Chuan-ju Liu
      - Peter Lengyel
suggested_experiments:
  - hypothesis: >-
      Ifi204 has distinct, non-redundant functions from cGAS in cytosolic DNA
      sensing, possibly through direct recruitment of STING via its PYRIN domain.
    description: >-
      Generate cGAS/Ifi204 double-knockout macrophages and compare type I IFN
      responses to bacterial DNA with single knockouts. Test whether Ifi204
      PYRIN domain mutants can still cooperate with cGAS using domain-swap
      constructs.
    experiment_type: genetic interaction analysis
  - hypothesis: >-
      The acetylation-dependent nuclear-to-cytoplasmic translocation of Ifi204
      is the critical switch between its transcriptional and innate immune
      functions.
    description: >-
      Identify the specific acetylation sites on Ifi204 using mass spectrometry
      after bacterial infection. Generate acetylation-mimicking and
      acetylation-deficient mutants and test their effects on IFN-beta
      production, STING recruitment, and transcriptional coactivator function.
    experiment_type: site-directed mutagenesis with functional assays