VIN3 (VERNALIZATION INSENSITIVE 3) is a nuclear PHD-superdomain/fibronectin III/VEL-domain protein of Arabidopsis whose transcription is induced only slowly during prolonged cold. This makes VIN3 accumulation a molecular readout of the length of winter. VIN3 forms a heterodimer with its constitutively expressed paralog VRN5/VIL1 and joins a PHD-PRC2 complex (VRN2, SWN/CLF, FIE, MSI1, VRN5, VEL1) at a small nucleation region near the first exon-intron boundary of the floral repressor FLC. There it is required for histone deacetylation and local H3K27me3 nucleation, which switches FLC alleles into a metastable silenced state that is later spread and maintained by other Polycomb factors. Its VEL domain undergoes head-to-tail polymerization that builds dynamic nuclear assemblies, and this is needed for multivalent chromatin association and efficient nucleation. Its PHD superdomain does not bind histone H3 tails. VIN3 also contributes to survival under hypoxia.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001666 response to hypoxia | IMP PMID:19392705 VERNALIZATION INSENSITIVE 3 (VIN3) is required for the respo... | KEEP AS NON CORE | Summary: Hypoxia induces VIN3, and vin3 seedlings survive 72 h of low oxygen less well; complementation rescues this. Reason: The survival phenotype is real and was complemented, but the mechanism is unknown, and loss of VIN3 does not change the known hypoxia-responsive transcripts. This is a secondary stress role, separate from VIN3's core role in FLC silencing. Supporting Evidence: PMID:19392705 Without VIN3 activity, fewer seedlings survived following a 72-h period of hypoxic treatment, indicating that VIN3 is required for the survival of Arabidopsis thaliana in response to hypoxic stress. |
| GO:0005515 protein binding | IPI PMID:16983073 The Arabidopsis thaliana vernalization response requires a p... | REMOVE | Summary: VIN3 co-purifies with VRN2 in a large PRC2-like complex during vernalization. Reason: GO:0005515 protein binding is uninformative. The interaction is real, but what it means (membership of the VIN3-containing PHD-PRC2 complex) is already captured by the chromatin silencing complex annotation. Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:16983073 We show in planta that VRN2 and VIN3 are part of a large protein complex that can include the PcG proteins FERTILIZATION INDEPENDENT ENDOSPERM, CURLY LEAF, and SWINGER. |
| GO:0005515 protein binding | IPI PMID:17114575 A PHD finger protein involved in both the vernalization and ... | MODIFY | Summary: VIN3 interacts with VIL1/VRN5 through the conserved C-terminal VEL domain. This was found in a yeast two-hybrid screen and confirmed for the native proteins. Reason: The cited work and Greb et al. 2007 support a specific VIN3-VRN5 heterodimer formed through the VEL domains. Protein heterodimerization activity says more than protein binding. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:17114575 Here we show that a related PHD finger-containing protein, VIN3-LIKE 1 (VIL1), identified in a screen for proteins that interact with VIN3, cooperates with VIN3 in the vernalization-mediated repression of FLC . PMID:17114575 That the screen identified clones containing only the conserved C-terminal domain of VIL1 indicated that this region is sufficient to mediate the interaction with VIN3. PMID:17174094 Our results suggest that during the prolonged cold, VRN5 and VIN3 form a heterodimer necessary for establishing the vernalization-induced chromatin modifications, histone deacetylation, and H3 lysine 27 trimethylation required for the epigenetic silencing of FLC. |
| GO:0005515 protein binding | IPI PMID:17114575 A PHD finger protein involved in both the vernalization and ... | MODIFY | Summary: VIN3 also interacts with the third VEL-family protein, VEL1/VIL2. The VEL domains interact with each other and with themselves. Reason: This is a VEL-domain heterotypic interaction between family members, and later structural work shows it is head-to-tail polymerization. Protein heterodimerization activity is more informative than protein binding. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:17114575 That the screen identified clones containing only the conserved C-terminal domain of VIL1 indicated that this region is sufficient to mediate the interaction with VIN3. PMID:36351412 VEL proteins contain a domain related to an atypical four-helix bundle that engages in spontaneous concentration-dependent head-to-tail polymerization to assemble dynamic biomolecular condensates. |
| GO:0005515 protein binding | IPI PMID:17174094 The PHD finger protein VRN5 functions in the epigenetic sile... | MODIFY | Summary: VIN3 and VRN5 form a heterodimer during prolonged cold. Reason: The source paper explicitly describes a VIN3-VRN5 heterodimer, so protein heterodimerization activity is the informative term. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:17174094 Our results suggest that during the prolonged cold, VRN5 and VIN3 form a heterodimer necessary for establishing the vernalization-induced chromatin modifications, histone deacetylation, and H3 lysine 27 trimethylation required for the epigenetic silencing of FLC. |
| GO:0005515 protein binding | IPI PMID:19452453 Proteomic profiling of tandem affinity purified 14-3-3 prote... | REMOVE | Summary: A high-throughput tandem-affinity purification of 14-3-3 (GRF2) complexes recovered VIN3. Reason: This is a generic protein-binding annotation from a proteomic screen centred on 14-3-3 proteins. No functional consequence is known, and the term is uninformative. |
| GO:0005634 nucleus | IDA PMID:17174094 The PHD finger protein VRN5 functions in the epigenetic sile... | ACCEPT | Summary: VIN3 is nuclear, as expected for a PRC2 accessory protein that associates with FLC chromatin. Supporting Evidence: PMID:17174094 Our results suggest that during the prolonged cold, VRN5 and VIN3 form a heterodimer necessary for establishing the vernalization-induced chromatin modifications, histone deacetylation, and H3 lysine 27 trimethylation required for the epigenetic silencing of FLC. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Nuclear localization from the UniProt subcellular location mapping; consistent with experimental data. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP prediction of nuclear localization; consistent with experimental data. |
| GO:0005677 chromatin silencing complex | IBA GO_REF:0000033 | ACCEPT | Summary: The PAINT node for the VEL clade (VIN3, VRN5, VEL1) places these proteins in a chromatin silencing (PRC2-associated) complex. VIN3 is itself one of the experimental descendants. Reason: This agrees with the purification of the PHD-PRC2 complex. Supporting Evidence: PMID:18854416 during prolonged cold a PHD-PRC2 complex forms composed of core PRC2 components (VRN2, SWINGER ... FIE ... MSI1 ... and three related PHD finger proteins, VRN5, VIN3, and VEL1. |
| GO:0005677 chromatin silencing complex | IDA PMID:18854416 A PHD-polycomb repressive complex 2 triggers the epigenetic ... | ACCEPT | Summary: VIN3 was purified as a component of the cold-formed PHD-PRC2 complex, together with VRN2, SWN, FIE, MSI1, VRN5 and VEL1. Supporting Evidence: PMID:18854416 during prolonged cold a PHD-PRC2 complex forms composed of core PRC2 components (VRN2, SWINGER ... FIE ... MSI1 ... and three related PHD finger proteins, VRN5, VIN3, and VEL1. |
| GO:0009409 response to cold | IEP PMID:16983073 The Arabidopsis thaliana vernalization response requires a p... | ACCEPT | Summary: VIN3 transcript and the VRN2/VIN3 complex accumulate during cold. Reason: Cold induction of VIN3 is the key way in which the duration of cold is read out. Response to cold is a valid parent of vernalization response. Supporting Evidence: PMID:16983073 The abundance of the complex increases during vernalization and declines after plants are returned to higher temperatures, consistent with the complex having a role in establishing FLC repression. file:ARATH/VIN3/VIN3-uniprot.txt INDUCTION: By cold. Expressed only after a duration of cold exposure |
| GO:0009409 response to cold | IEP PMID:17114575 A PHD finger protein involved in both the vernalization and ... | ACCEPT | Summary: VIN3 expression is induced by prolonged cold. Supporting Evidence: file:ARATH/VIN3/VIN3-uniprot.txt INDUCTION: By cold. Expressed only after a duration of cold exposure |
| GO:0010048 vernalization response | IBA GO_REF:0000033 | ACCEPT | Summary: Vernalization response, placed by PAINT on the VIN3/VRN5 node. Both genes have strong experimental support. Supporting Evidence: PMID:14712276 Here we identify a gene with a function in the measurement of the duration of cold exposure and in the establishment of the vernalized state. |
| GO:0010048 vernalization response | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro VIN3-like family mapping to vernalization response; correct for this protein. |
| GO:0010048 vernalization response | IEP PMID:16983073 The Arabidopsis thaliana vernalization response requires a p... | ACCEPT | Summary: Expression-based support for a role in vernalization. Supporting Evidence: PMID:16983073 The abundance of the complex increases during vernalization and declines after plants are returned to higher temperatures, consistent with the complex having a role in establishing FLC repression. |
| GO:0010048 vernalization response | IMP PMID:17114575 A PHD finger protein involved in both the vernalization and ... | ACCEPT | Summary: vin3 mutants fail to respond to vernalization; this is VIN3's defining phenotype. Supporting Evidence: PMID:17114575 Here we show that a related PHD finger-containing protein, VIN3-LIKE 1 (VIL1), identified in a screen for proteins that interact with VIN3, cooperates with VIN3 in the vernalization-mediated repression of FLC . |
| GO:0010048 vernalization response | IMP PMID:17174094 The PHD finger protein VRN5 functions in the epigenetic sile... | ACCEPT | Summary: vin3 mutants are impaired in vernalization-induced FLC silencing. Supporting Evidence: PMID:17174094 Our results suggest that during the prolonged cold, VRN5 and VIN3 form a heterodimer necessary for establishing the vernalization-induced chromatin modifications, histone deacetylation, and H3 lysine 27 trimethylation required for the epigenetic silencing of FLC. |
| GO:0016607 nuclear speck | IDA PMID:17174094 The PHD finger protein VRN5 functions in the epigenetic sile... | ACCEPT | Summary: VIN3 (with VRN5) localizes to nuclear speckles/foci. This fits with the later finding that VEL-domain polymerization assembles nuclear condensates. Supporting Evidence: PMID:36351412 VEL proteins contain a domain related to an atypical four-helix bundle that engages in spontaneous concentration-dependent head-to-tail polymerization to assemble dynamic biomolecular condensates. |
| GO:0016607 nuclear speck | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping (nucleus speckle); consistent with IDA. |
| GO:0040029 epigenetic regulation of gene expression | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro mapping to epigenetic regulation of gene expression; correct, if broad. |
| GO:0045814 negative regulation of gene expression, epigenetic | IMP PMID:17174094 The PHD finger protein VRN5 functions in the epigenetic sile... | ACCEPT | Summary: VIN3 is required for vernalization-induced histone deacetylation and H3K27me3 nucleation that epigenetically silence FLC. Supporting Evidence: PMID:17174094 Our results suggest that during the prolonged cold, VRN5 and VIN3 form a heterodimer necessary for establishing the vernalization-induced chromatin modifications, histone deacetylation, and H3 lysine 27 trimethylation required for the epigenetic silencing of FLC. PMID:28818969 a subset of Polycomb repressive complex 2 factors nucleate silencing in a small region within FLC, locally increasing H3K27me3 levels. |
| GO:0070417 cellular response to cold | IEP PMID:17174094 The PHD finger protein VRN5 functions in the epigenetic sile... | ACCEPT | Summary: Cold induction of VIN3 expression. Supporting Evidence: file:ARATH/VIN3/VIN3-uniprot.txt INDUCTION: By cold. Expressed only after a duration of cold exposure |
| GO:0140006 histone H3 reader activity | IBA GO_REF:0000033 | REMOVE | Summary: IBA histone H3 reader activity for the VEL clade, seeded from VEL1 (AT4G30200). Reason: Direct structural and biophysical work contradicts this for VIN3. Crystal structures show that the VEL PHD finger is part of a tripartite PHD superdomain with no canonical three-pronged histone-binding pocket. ITC and NMR detected no binding of the Arabidopsis VIN3 PHD superdomain, or of its minimal PHD finger, to unmodified or modified H3 tails. An earlier pull-down result suggesting H3 binding is superseded by these quantitative assays. VIN3 is therefore outside the clade that inherited H3-reader activity, despite the PHD signature. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN008198652 SUPPORTS SOURCE BUT NOT TARGET VEL-clade node; H3-reader IBD seeded only from VEL1 (AT4G30200). Structural and ITC/NMR data show the VEL PHD superdomain, including that of At VIN3, does not bind H3 tails. AGI_LocusCode:AT4G30200 SOURCE WEAK OR INFERRED VEL1 seed; the H3-binding claim for VEL PHD fingers rests on earlier pull-down assays that later quantitative ITC/NMR could not reproduce for VIN3. Supporting Evidence: PMID:36174674 This VEL PHD superdomain neither binds to unmodified nor variously modified histone H3 tails, as demonstrated by isothermal calorimetry and NMR spectroscopy. PMID:36174674 Indeed, using ITC and NMR spectroscopy, we were unable to detect binding of the purified VIN3 PHD superdomain nor of its minimal PHD finger to various modified and unmodified histone H3 tail peptides. |
| GO:0140719 constitutive heterochromatin formation | IBA GO_REF:0000033 | MODIFY | Summary: IBA constitutive heterochromatin formation for the VEL clade. Reason: The VEL proteins act in Polycomb (H3K27me3) silencing of developmental genes such as FLC. This is facultative, not constitutive, heterochromatin formation. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008198652 SUPPORTS TRANSFER The heterochromatin-formation role of the VEL clade is inherited correctly, but in the Polycomb (facultative) sense rather than the constitutive one. Proposed replacements: facultative heterochromatin formation Supporting Evidence: PMID:28818969 a subset of Polycomb repressive complex 2 factors nucleate silencing in a small region within FLC, locally increasing H3K27me3 levels. PMID:36351412 Mutations blocking polymerization of this VEL domain prevent Polycomb silencing at FLC. |
| GO:0140693 molecular condensate scaffold activity | IDA PMID:40858112 VEL-dependent polymerization maintains the chromatin associa... | NEW | Summary: VIN3 VEL-domain head-to-tail polymerization assembles dynamic biomolecular condensates (in heterologous cells) and higher-order nuclear VIN3 assemblies in planta that are required for efficient H3K27me3 nucleation. Reason: Molecular condensate scaffold activity describes how the VEL domain works: it self-assembles and recruits PRC2 accessories into multivalent assemblies. Polymerization-blocking mutations abolish FLC silencing. Supporting Evidence: PMID:36351412 VEL proteins contain a domain related to an atypical four-helix bundle that engages in spontaneous concentration-dependent head-to-tail polymerization to assemble dynamic biomolecular condensates. PMID:40858112 We show that VIN3 VEL polymerization produces higher-order nuclear VIN3 assemblies in vivo, which promote multivalent chromatin association and efficient H3K27me3 nucleation. PMID:36351412 Mutations blocking polymerization of this VEL domain prevent Polycomb silencing at FLC. |
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Download this section (compressed HTML)Q: What controls the slow, quantitative induction of VIN3 transcription during prolonged cold (the cold-duration sensor), and how is it reset in warm conditions?
Q: Does the positively charged VEL PHD superdomain bind nucleic acids (DNA or COOLAIR RNA) in vivo, replacing the canonical histone-reader function?
Experiment: Test binding of purified VIN3 PHD superdomain to DNA, nucleosomes and COOLAIR RNA in vitro. Complement vin3 with charge-reversal PHD mutants and assay H3K27me3 nucleation at FLC by ChIP-qPCR.
Hypothesis: The VIN3 PHD superdomain contacts FLC chromatin via nucleic-acid binding rather than histone tails.
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