VRN2 (VERNALIZATION 2) is a nuclear Polycomb group protein of Arabidopsis, one of three Su(z)12 homologs (with EMF2 and FIS2) with a SUZ12-type zinc finger and a VEFS box. It is a core subunit of VRN2-PRC2 complexes, together with the E(z) methyltransferases CLF or SWN, the ESC homolog FIE and the p55 homolog MSI1. VRN2 associates with the FLC locus independently of cold. During prolonged cold it joins the VEL-family accessories VIN3, VRN5 and VEL1 to form PHD-PRC2, which nucleates H3K27me3 in a small region of FLC; after return to warmth the mark spreads over the locus. VRN2 is therefore needed for FLC to stay repressed after winter, the cellular memory of vernalization, rather than for its initial cold-dependent down-regulation. VRN2 acts partly redundantly with EMF2 in vegetative Polycomb silencing more generally.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001222 transcription corepressor binding | IPI PMID:28825728 Cis and trans determinants of epigenetic silencing by Polyco... | MODIFY | Summary: Xiao et al. 2017 show that PRE-binding transcription factors physically interact with and recruit PRC2. The GOA row records VRN2 binding to the MADS-box transcription factor AGAMOUS (AT4G18960). Reason: The interacting partner given in GOA is AGAMOUS, a DNA-binding MADS-box transcription factor, not a transcriptional corepressor. The supported claim is that a PRC2 Su(z)12 subunit binds a sequence-specific transcription factor that recruits it, so DNA-binding transcription factor binding is the more accurate term. The full text was not available, so the specific assay is not re-adjudicated. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:28825728 We identify transcription factor families that bind to these PREs, colocalize with PRC2 on chromatin, physically interact with and recruit PRC2, and are required for PRC2-mediated gene silencing in vivo. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | REMOVE | Summary: Assignment of VRN2 as a DNA-binding transcription factor in a genome-wide transcription-factor catalog, based on its zinc finger. Reason: VRN2 is a Su(z)12/VEFS-family Polycomb group protein that acts as a core PRC2 subunit. No evidence shows sequence-specific DNA-binding transcription factor activity. Its C2H2-type zinc finger is the conserved SUZ12 zinc-finger module, not a TF DNA-binding domain. PRC2 is recruited to targets by separate sequence-specific transcription factors. Supporting Evidence: PMID:11719192 The VERNALIZATION2 (VRN2) gene mediates vernalization and encodes a nuclear-localized zinc finger protein with similarity to Polycomb group (PcG) proteins of plants and animals. PMID:26642436 Using tagged CLF we identified EMF2 and VRN2 ... confirming that CLF occurs in both VRN2-PRC2 and EMF2-PRC2 complexes in vivo. PMID:28825728 We identify transcription factor families that bind to these PREs, colocalize with PRC2 on chromatin, physically interact with and recruit PRC2, and are required for PRC2-mediated gene silencing in vivo. |
| GO:0005515 protein binding | IPI PMID:15456723 Interaction of Polycomb-group proteins controlling flowering... | REMOVE | Summary: Yeast two-hybrid interaction of VRN2 with CLF. Reason: GO:0005515 protein binding is uninformative. The interaction itself is credible (VRN2 is the Su(z)12-type subunit of VRN2-PRC2), but membership of PRC2 is better captured by the complex annotations (chromatin silencing complex; ESC/E(Z) complex). Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:15456723 Analysis in yeast further indicates a potential for the CLF and SWN proteins to interact with the other VEFS domain proteins VRN2 and FIS2. |
| GO:0005515 protein binding | IPI PMID:15456723 Interaction of Polycomb-group proteins controlling flowering... | REMOVE | Summary: Yeast two-hybrid interaction of VRN2 with SWN. Reason: GO:0005515 protein binding is uninformative. The interaction itself is credible (VRN2 is the Su(z)12-type subunit of VRN2-PRC2), but membership of PRC2 is better captured by the complex annotations (chromatin silencing complex; ESC/E(Z) complex). Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:15456723 Analysis in yeast further indicates a potential for the CLF and SWN proteins to interact with the other VEFS domain proteins VRN2 and FIS2. |
| GO:0005515 protein binding | IPI PMID:16983073 The Arabidopsis thaliana vernalization response requires a p... | REMOVE | Summary: In planta co-purification of VRN2 with CLF. Reason: GO:0005515 protein binding is uninformative. The interaction itself is credible (VRN2 is the Su(z)12-type subunit of VRN2-PRC2), but membership of PRC2 is better captured by the complex annotations (chromatin silencing complex; ESC/E(Z) complex). 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:16983073 The Arabidopsis thaliana vernalization response requires a p... | REMOVE | Summary: In planta co-purification of VRN2 with VIN3. Reason: GO:0005515 protein binding is uninformative. The interaction itself is credible (VRN2 is the Su(z)12-type subunit of VRN2-PRC2), but membership of PRC2 is better captured by the complex annotations (chromatin silencing complex; ESC/E(Z) complex). 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:16983073 The Arabidopsis thaliana vernalization response requires a p... | REMOVE | Summary: In planta co-purification of VRN2 with FIE. Reason: GO:0005515 protein binding is uninformative. The interaction itself is credible (VRN2 is the Su(z)12-type subunit of VRN2-PRC2), but membership of PRC2 is better captured by the complex annotations (chromatin silencing complex; ESC/E(Z) complex). 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:16983073 The Arabidopsis thaliana vernalization response requires a p... | REMOVE | Summary: In planta co-purification of VRN2 with SWN. Reason: GO:0005515 protein binding is uninformative. The interaction itself is credible (VRN2 is the Su(z)12-type subunit of VRN2-PRC2), but membership of PRC2 is better captured by the complex annotations (chromatin silencing complex; ESC/E(Z) complex). 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:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: ALP1, a domesticated PIF/Harbinger transposase that antagonises PcG silencing, co-purifies with core CLF/SWN-PRC2 components including VRN2. Reason: GO:0005515 protein binding is uninformative. The interaction itself is credible (VRN2 is the Su(z)12-type subunit of VRN2-PRC2), but membership of PRC2 is better captured by the complex annotations (chromatin silencing complex; ESC/E(Z) complex). Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:26642436 By contrast, ALP1 associates with the core components of the CLF and SWN containing PRC2 complexes in vivo but not with EMF1 and LHP1. |
| GO:0005634 nucleus | IDA PMID:11719192 The VERNALIZATION 2 gene mediates the epigenetic regulation ... | ACCEPT | Summary: VRN2 is a nuclear-localized protein. Supporting Evidence: PMID:11719192 The VERNALIZATION2 (VRN2) gene mediates vernalization and encodes a nuclear-localized zinc finger protein with similarity to Polycomb group (PcG) proteins of plants and animals. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Automated nuclear localization; 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 node for the VEFS/Su(z)12 family (including mouse Suz12) placing members in a chromatin silencing complex; VRN2 is an experimental descendant. 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: VRN2 is a core subunit of the purified 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:0006325 chromatin organization | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA assignment to chromatin organization; correct but broad (VRN2-PRC2 deposits H3K27me3). |
| GO:0006346 DNA methylation-dependent constitutive heterochromatin formation | IBA GO_REF:0000033 | MODIFY | Summary: IBA DNA methylation-dependent constitutive heterochromatin formation, seeded from FIS2 (AT2G35670). Reason: VRN2-PRC2 represses developmental genes such as FLC by H3K27 trimethylation. This is facultative heterochromatin, and the DNA-methylation dependence seen for the seed-specific FIS2-PRC2 at imprinted loci is not established for VRN2. The process inherited by the VEFS family is Polycomb facultative heterochromatin formation. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: CONTEXT OR TISSUE MISMATCH GRANULARITY MISMATCH Sources checked: PANTHER:PTN000502888 SUPPORTS TRANSFER VEFS/Su(z)12 node; heterochromatin-formation role is inherited, but in the Polycomb facultative sense. AGI_LocusCode:AT2G35670 SUPPORTS SOURCE BUT NOT TARGET FIS2 seed: FIS2-PRC2 acts at seed imprinted loci interplaying with DNA methylation; that context is specific to the FIS2 complex. Proposed replacements: facultative heterochromatin formation Supporting Evidence: PMID:18854416 The PHD-PRC2 activity increases H3K27me3 throughout the locus to levels sufficient for stable silencing. PMID:26642436 MEA and FIS2 act specifically in seed, whereas CLF and SWN show overlapping and partially redundant roles in the plant body as do EMF2 and VRN2 |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000108 | MODIFY | Summary: Inferred from the (incorrect) DNA-binding transcription factor activity annotation. Reason: VRN2 does regulate transcription, but as part of Polycomb silencing rather than as a TF. The informative process is epigenetic negative regulation of gene expression. Proposed replacements: negative regulation of gene expression, epigenetic Supporting Evidence: PMID:11719192 VRN2 function therefore stably maintains FLC repression after a cold treatment, serving as a mechanism for the cellular memory of vernalization. |
| GO:0009409 response to cold | IEP PMID:16983073 The Arabidopsis thaliana vernalization response requires a p... | KEEP AS NON CORE | Summary: The VRN2-VIN3 complex increases in abundance during cold, mainly because VIN3 is induced; VRN2 itself is expressed with or without vernalization. Reason: VRN2's role in cold responses is limited to the vernalization response. The IEP reflects complex abundance rather than induction of VRN2 by cold. 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:8998499 Arabidopsis mutants showing an altered response to vernaliza... | ACCEPT | Summary: vrn2 was isolated as a mutant with reduced vernalization response; VRN2 is needed to maintain FLC repression after cold. Supporting Evidence: PMID:8998499 Allelism tests showed that these mutations fall into at least three complementation groups defining three loci named VRN 1, 2 and 3. PMID:11719192 In vrn2 mutants, FLC expression is downregulated normally in response to vernalization, but instead of remaining low, FLC mRNA levels increase when plants are returned to normal temperatures. |
| GO:0031490 chromatin DNA binding | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA chromatin DNA binding from the Su(z)12 family node (mouse Suz12 donor). Reason: VRN2 associates with FLC chromatin across the locus independently of cold, consistent with chromatin association of the Su(z)12 subunit. Direct DNA binding by VRN2 has not been shown, so this is kept as non-core. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000502888 SUPPORTS TRANSFER Su(z)12-family node; chromatin association is consistent with VRN2 ChIP data. Supporting Evidence: PMID:18854416 Here we show that, contrary to expectations, VRN2 associates throughout the FLC locus independently of cold. |
| GO:0141044 epigenetic programming in the endosperm | IMP PMID:16527743 Polycomb group complexes self-regulate imprinting of the Pol... | KEEP AS NON CORE | Summary: PcG complexes self-regulate imprinting of MEDEA; vegetative PcG activity (in which VRN2 is a candidate Su(z)12 subunit) keeps MEA silenced. Reason: The paper is abstract-only here, so the specific vrn2 data cannot be inspected; we defer to the curator. VRN2's main role is vegetative silencing of FLC, and any contribution to MEA imprinting is secondary and likely redundant with EMF2. Supporting Evidence: PMID:16527743 We show that Pc-G complexes maintain MEA transcription silenced throughout vegetative life and male gametogenesis. |
| GO:0035098 ESC/E(Z) complex | IDA PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | NEW | Summary: VRN2 is the Su(z)12-type subunit of a VRN2-PRC2 complex co-purified with CLF, FIE and MSI1 in vivo, and of the cold-formed PHD-PRC2 with SWN, FIE and MSI1. Reason: ESC/E(Z) complex (PRC2) is more specific than the existing chromatin silencing complex annotation and names the complex VRN2 is a core subunit of. Supporting Evidence: PMID:26642436 Using tagged CLF we identified EMF2 and VRN2 ... confirming that CLF occurs in both VRN2-PRC2 and EMF2-PRC2 complexes in vivo. 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. |
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Download this section (compressed HTML)Q: What distinguishes VRN2-PRC2 from EMF2-PRC2 in target specificity, and why is VRN2 specifically required at FLC?
Q: Does VRN2 contact the VRN5 PHD-FNIII module directly, and is this the sole route by which VEL proteins join PRC2?
Experiment: Make VRN2/EMF2 domain swaps, express them in vrn2 emf2-weak backgrounds, and assay VRN5/VIN3 co-IP, H3K27me3 nucleation at FLC and stable silencing after cold.
Hypothesis: VRN2-specific sequences outside the VEFS box confer FLC targeting and VEL-protein binding.
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