VRN5 (VERNALIZATION 5; also VIN3-LIKE 1, VIL1) is a constitutively expressed nuclear VEL-family protein of Arabidopsis with an atypical PHD superdomain, a fibronectin III domain and a C-terminal VEL polymerization domain. It is an accessory subunit of plant Polycomb Repressive Complex 2. VRN5 binds the PRC2 core (via VRN2) through its compact PHD-superdomain/FNIII module and heterodimerizes with the cold-induced paralog VIN3 through the VEL domain, so it bridges VIN3 to PRC2. During prolonged cold, VRN5 associates, in a VIN3-dependent way, with a small nucleation region in FLC intron 1, where the resulting PHD-PRC2 complex deposits H3K27me3. After return to warmth, VRN5 spreads across the FLC locus as H3K27me3 increases, stably silencing FLC. VRN5 also contributes to Polycomb silencing of the related floral repressor FLM, which promotes flowering in short days.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:17114575 A PHD finger protein involved in both the vernalization and ... | MODIFY | Summary: VRN5/VIL1 was identified as a VIN3 interactor in a yeast two-hybrid screen; the conserved C-terminal VEL domain is sufficient for the interaction. Reason: This is a specific VEL-domain heterodimer with VIN3, so 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: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: VRN5 also interacts with the paralog VEL1/VIL2 through the VEL domain. Reason: This is a heterotypic VEL-domain interaction between paralogs, better captured by protein heterodimerization activity. 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. |
| GO:0005515 protein binding | IPI PMID:17174094 The PHD finger protein VRN5 functions in the epigenetic sile... | MODIFY | Summary: VRN5 and VIN3 form a heterodimer during prolonged cold. Reason: The source paper explicitly describes the VRN5-VIN3 heterodimer. 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:0005634 nucleus | IDA PMID:17174094 The PHD finger protein VRN5 functions in the epigenetic sile... | ACCEPT | Summary: VRN5 is nuclear and associates with FLC chromatin. Supporting Evidence: PMID:18854416 The vernalization-induced silencing is triggered by the cold-dependent association of the PHD finger protein VRN5 to a specific domain in FLC intron 1, and this association is dependent on the cold-induced PHD protein VIN3. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to nucleus; consistent with IDA. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP nuclear prediction; consistent with IDA. |
| GO:0005677 chromatin silencing complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT VEL-clade node; VRN5 is itself an experimental descendant (PHD-PRC2 purification). 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: VRN5 was the tagged bait used to purify the cold-formed PHD-PRC2 complex (VRN2, SWN, FIE, MSI1, VRN5, VIN3, 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:17114575 A PHD finger protein involved in both the vernalization and ... | KEEP AS NON CORE | Summary: VIL1 expression is only slightly increased by long cold exposure, unlike the strong induction of VIN3. Reason: The expression change is weak, and VRN5 acts largely as a constitutively expressed PRC2 accessory. VIN3 carries the cold-dependent induction. Supporting Evidence: file:ARATH/VRN5/VRN5-uniprot.txt Slightly induced by long cold exposure |
| GO:0010048 vernalization response | IBA GO_REF:0000033 | ACCEPT | Summary: Vernalization response, inherited at the VIN3/VRN5 node; experimentally supported for VRN5. 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:0010048 vernalization response | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro VIN3-like mapping; correct for VRN5. |
| GO:0010048 vernalization response | IMP PMID:17114575 A PHD finger protein involved in both the vernalization and ... | ACCEPT | Summary: vil1 mutants are vernalization-insensitive and fail to silence FLC/FLM. Supporting Evidence: PMID:17114575 In the vernalization pathway, VIL1, along with VERNALIZATION INSENSITIVE 3 (VIN3), is necessary for the modifications to FLC and FLM chromatin that are associated with an epigenetically silenced state and with acquisition of competence to flower. |
| GO:0010048 vernalization response | IMP PMID:17174094 The PHD finger protein VRN5 functions in the epigenetic sile... | ACCEPT | Summary: vrn5 mutants misexpress FLC at the end of cold and after return to warm. 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: VRN5 localizes to nuclear speckles, consistent with VEL-domain-driven nuclear assemblies. 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 | 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. |
| GO:0040029 epigenetic regulation of gene expression | IMP PMID:17114575 A PHD finger protein involved in both the vernalization and ... | ACCEPT | Summary: VIL1 is required for the chromatin modifications associated with epigenetic silencing of FLC and FLM. Supporting Evidence: PMID:17114575 In the vernalization pathway, VIL1, along with VERNALIZATION INSENSITIVE 3 (VIN3), is necessary for the modifications to FLC and FLM chromatin that are associated with an epigenetically silenced state and with acquisition of competence to flower. |
| GO:0045814 negative regulation of gene expression, epigenetic | IMP PMID:17174094 The PHD finger protein VRN5 functions in the epigenetic sile... | ACCEPT | Summary: VRN5 is required for vernalization-induced histone deacetylation and H3K27me3 at FLC; it binds the FLC nucleation region and later spreads over the locus. 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:18854416 In plants returned to warm conditions, VRN5 distribution changes, and it associates more broadly over FLC, coincident with significant increases in H3K27me3. |
| GO:0048572 short-day photoperiodism | IMP PMID:17114575 A PHD finger protein involved in both the vernalization and ... | KEEP AS NON CORE | Summary: VIL1 represses FLM in a photoperiod-dependent manner; vil1 mutants flower late in short days. Reason: This is a real but secondary output of VRN5's general PRC2-accessory role (silencing of the FLC-clade gene FLM), not a distinct photoperiod-sensing function. Supporting Evidence: PMID:17114575 In addition, VIL1 regulates FLM independently of VIN3 in a photoperiod-dependent manner. |
| GO:0048575 short-day photoperiodism, flowering | IMP PMID:17114575 A PHD finger protein involved in both the vernalization and ... | KEEP AS NON CORE | Summary: Short-day flowering phenotype of vil1, mediated through FLM. Reason: Same reasoning as for short-day photoperiodism: this is downstream of Polycomb silencing of FLM. Supporting Evidence: PMID:17114575 In addition, VIL1 regulates FLM independently of VIN3 in a photoperiod-dependent manner. |
| GO:0140006 histone H3 reader activity | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA histone H3 reader activity for the VEL clade, seeded from VEL1. Reason: Structural work shows that the VEL PHD finger sits inside a tripartite PHD superdomain that lacks the canonical H3-binding pocket. The VIN3 superdomain bound no H3 tails by ITC/NMR. The VRN5 superdomain itself was not assayed, but in VRN5 this module packs against the FNIII domain and mediates binding to PRC2 core (VRN2), not to histones. H3-reader activity is therefore unlikely to be a VRN5 function. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN008198652 SUPPORTS SOURCE BUT NOT TARGET VEL-clade node; the H3-reader IBD rests on VEL1 pull-down data, while VEL PHD superdomains lack the H3-binding architecture. 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:40858112 specifically in VRN5, there is a close packing of the central PHD superdomain and FNIII domain, and this mediates its interaction with a PRC2 core complex with the core subunit VRN2 |
| GO:0140719 constitutive heterochromatin formation | IBA GO_REF:0000033 | MODIFY | Summary: IBA constitutive heterochromatin formation for the VEL clade. Reason: VRN5 acts in Polycomb/H3K27me3 silencing of developmental genes (FLC, FLM). This is facultative heterochromatin. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008198652 SUPPORTS TRANSFER The heterochromatin role is inherited, but in the facultative (Polycomb) sense. 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: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:0030674 protein-macromolecule adaptor activity | IMP PMID:40858112 VEL-dependent polymerization maintains the chromatin associa... | NEW | Summary: VRN5 is required to physically connect VIN3 with PRC2: its compact PHD-superdomain/FNIII module binds the PRC2 core (VRN2), and its VEL domain binds VIN3. Reason: VRN5 bridges the cold-induced VIN3 to the PRC2 core, which is an adaptor role. This is more specific than generic protein binding and is the main way VRN5 differs from VIN3. Supporting Evidence: PMID:40858112 VRN5 VEL polymerization, however, is not required unless a third homolog VEL1 is absent. The VRN5 VEL domain has different polymerization properties and is functionally unable to replace VIN3 VEL, but it is required to physically connect VIN3 with PRC2. PMID:40858112 specifically in VRN5, there is a close packing of the central PHD superdomain and FNIII domain, and this mediates its interaction with a PRC2 core complex with the core subunit VRN2 |
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Download this section (compressed HTML)Q: Which VRN5 surface contacts VRN2 in the PRC2 core, and is this interaction cold-regulated or constitutive?
Q: How is VRN5 targeted to FLM and other Polycomb targets independently of VIN3 (e.g. in short days)?
Experiment: Map the VRN5-VRN2 interface by crosslinking-MS or structure prediction plus mutagenesis. Complement vrn5 with interface mutants and test PRC2 co-IP, VIN3 co-IP and FLC H3K27me3 nucleation after cold.
Hypothesis: The VRN5 PHD-FNIII interface is required for PRC2 binding and FLC silencing, but not for VIN3 heterodimerization.
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