VRN1 (VERNALIZATION 1) is a nuclear Arabidopsis protein with two plant-specific B3 DNA-binding domains. Unlike most B3 proteins, it binds DNA without sequence specificity, through a defined positively charged surface on the second B3 domain. VRN1 associates broadly with euchromatic chromosomes (not chromocenters) in interphase and mitosis, but not in meiosis, independently of vernalization or VRN2. It is required to maintain the stable repression of the floral repressor FLC after winter cold: in vrn1 mutants FLC is down-regulated in the cold but reactivated afterwards. It needs vernalization-specific factors to act at FLC. VRN1 also has vernalization-independent roles in flowering (through FT, seen on overexpression) and, judging from dominant repressor fusions that overcome redundancy, in essential developmental processes.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | MODIFY | Summary: IBA transcription cis-regulatory region binding from the B3-domain (VRN1-like) family node. Reason: B3 domains in many family members bind specific cis-elements, but VRN1 binds DNA without sequence specificity, through a defined positively charged surface. It associates generally with chromosomes rather than with specific promoters. The supported activity is DNA binding. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN008641690 SUPPORTS SOURCE BUT NOT TARGET B3-domain family node; the cis-element specificity of the family is not retained by VRN1, which is sequence-nonspecific. Proposed replacements: DNA binding Supporting Evidence: PMID:12114624 VRN1 encodes a protein that binds DNA in vitro in a non-sequence-specific manner and functions in stable repression of the major target of the vernalization pathway, the floral repressor FLC. PMID:23255593 The triple mutant R249E/R289E/R296E was almost completely incapable of DNA binding in vitro. Thus, we have revealed that although VRN1 is sequence-nonspecific in DNA binding, it has a defined DNA-binding surface. |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:25352272 Promoter-based integration in plant defense regulation. | MODIFY | Summary: Large-scale yeast one-hybrid screen of defence-gene promoters recovered VRN1 binding to promoter fragments (AT1G62540 FMO GS-OX2, AT4G03060 AOP2). Reason: The binding observed in yeast is real, but VRN1 binds DNA without sequence specificity, so these one-hybrid hits probably reflect that general affinity rather than specific regulation of glucosinolate-pathway promoters. No in planta regulation of these targets by VRN1 has been shown. The supported activity is DNA binding. Proposed replacements: DNA binding |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:25533953 An Arabidopsis gene regulatory network for secondary cell wa... | MODIFY | Summary: Large-scale yeast one-hybrid screen (secondary cell wall network) recovered VRN1 binding to promoter fragments. Reason: Same reasoning as for the other one-hybrid row: these hits are consistent with sequence-nonspecific DNA binding, and the targets have no demonstrated biological relevance to VRN1 function. The supported activity is DNA binding. Proposed replacements: DNA binding |
| GO:0003677 DNA binding | IDA PMID:12114624 Multiple roles of Arabidopsis VRN1 in vernalization and flow... | ACCEPT | Summary: Recombinant VRN1 binds DNA in vitro in a non-sequence-specific manner. Supporting Evidence: PMID:12114624 VRN1 encodes a protein that binds DNA in vitro in a non-sequence-specific manner and functions in stable repression of the major target of the vernalization pathway, the floral repressor FLC. |
| GO:0003677 DNA binding | IDA PMID:23255593 The Arabidopsis B3 domain protein VERNALIZATION1 (VRN1) is i... | ACCEPT | Summary: Structure, NMR and mutagenesis define the DNA-binding surface of the second VRN1 B3 domain; the R249E/R289E/R296E triple mutant abolishes binding. Supporting Evidence: PMID:23255593 The triple mutant R249E/R289E/R296E was almost completely incapable of DNA binding in vitro. Thus, we have revealed that although VRN1 is sequence-nonspecific in DNA binding, it has a defined DNA-binding surface. |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: B3 domain-based DNA binding; consistent with IDA. |
| GO:0005634 nucleus | EXP PMID:12114624 Multiple roles of Arabidopsis VRN1 in vernalization and flow... | ACCEPT | Summary: VRN1 is a nuclear protein. Supporting Evidence: PMID:23255593 Despite the specific phenotype of genetic vrn1 mutants, the VERNALIZATION1 (VRN1) protein localizes throughout the nucleus and shows sequence-nonspecific binding in vitro. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear localization inherited in the B3-domain family; experimentally confirmed for VRN1. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN008641690 SUPPORTS TRANSFER Nuclear localization is shared across the B3 family and verified for VRN1. Supporting Evidence: PMID:23255593 Despite the specific phenotype of genetic vrn1 mutants, the VERNALIZATION1 (VRN1) protein localizes throughout the nucleus and shows sequence-nonspecific binding in vitro. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Automated nuclear localization; consistent with experimental data. |
| GO:0005654 nucleoplasm | IDA PMID:16549797 LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1,... | ACCEPT | Summary: VRN1 associates broadly with chromosomes (euchromatin, not chromocenters) throughout the nucleoplasm, including in mitosis. Supporting Evidence: PMID:16549797 We explored the localization of VRN1 and found it to be associated generally with Arabidopsis chromosomes but not the heterochromatic chromocenters. PMID:16549797 This association did not depend on vernalization or VRN2 function and was maintained during mitosis but was lost in meiotic chromosomes, suggesting that VRN1 may contribute to chromatin silencing that is not meiotically stable. |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA regulation of DNA-templated transcription from the B3 family. Reason: VRN1 is needed to keep FLC repressed after vernalization, and its overexpression affects FT. It is not known whether VRN1 regulates transcription directly or acts mainly through chromatin silencing. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN008641690 SUPPORTS TRANSFER Broad transcription-regulation term is compatible with VRN1's role, but the mechanism is unresolved. Supporting Evidence: PMID:12114624 VRN1 encodes a protein that binds DNA in vitro in a non-sequence-specific manner and functions in stable repression of the major target of the vernalization pathway, the floral repressor FLC. PMID:12114624 Overexpression of VRN1 reveals a vernalization-independent function for VRN1, mediated predominantly through the floral pathway integrator FT, and demonstrates that VRN1 requires vernalization-specific factors to target FLC. |
| GO:0009409 response to cold | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA assignment to response to cold. This is broad but correct, since vernalization (VRN1's role) is a response to prolonged cold. Reason: Vernalization response is_a response to cold, so the broader IEA is consistent. |
| GO:0009909 regulation of flower development | IMP PMID:12114624 Multiple roles of Arabidopsis VRN1 in vernalization and flow... | KEEP AS NON CORE | Summary: vrn1 mutants and VRN1 overexpression alter flowering time, partly through FT independently of vernalization. Reason: Real, but the vernalization-independent FT-mediated effect comes from overexpression. Repression of FLC within the vernalization response is the core role. Supporting Evidence: PMID:12114624 Overexpression of VRN1 reveals a vernalization-independent function for VRN1, mediated predominantly through the floral pathway integrator FT, and demonstrates that VRN1 requires vernalization-specific factors to target FLC. |
| GO:0010048 vernalization response | IBA GO_REF:0000033 | ACCEPT | Summary: Vernalization response placed on the VRN1-like node; VRN1 is the experimental donor. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN004899496 SUPPORTS TRANSFER VRN1-like node; VRN1's own experimental data ground the IBD. Supporting Evidence: PMID:12114624 VRN1 encodes a protein that binds DNA in vitro in a non-sequence-specific manner and functions in stable repression of the major target of the vernalization pathway, the floral repressor FLC. |
| GO:0010048 vernalization response | IMP PMID:8998499 Arabidopsis mutants showing an altered response to vernaliza... | ACCEPT | Summary: vrn1 was isolated as a mutant with reduced vernalization response. 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. |
| GO:0005694 chromosome | IDA PMID:16549797 LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1,... | NEW | Summary: VRN1 associates generally with chromosomes (not chromocenters), and the association persists through mitosis. Reason: Chromosome association is a distinctive, experimentally shown property of VRN1 that the nucleoplasm annotation does not capture. Supporting Evidence: PMID:16549797 We explored the localization of VRN1 and found it to be associated generally with Arabidopsis chromosomes but not the heterochromatic chromocenters. PMID:16549797 This association did not depend on vernalization or VRN2 function and was maintained during mitosis but was lost in meiotic chromosomes, suggesting that VRN1 may contribute to chromatin silencing that is not meiotically stable. |
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Download this section (compressed HTML)Q: Which vernalization-specific factors target the sequence-nonspecific VRN1 to FLC, and does VRN1 physically associate with PRC2, LHP1 or VAL1 at the nucleation region?
Q: What essential developmental processes are revealed by VRN1-SRDX, and which B3 paralogs act redundantly with VRN1?
Experiment: Profile VRN1 genome-wide by ChIP-seq before, during and after vernalization in wild type, vrn2 and lhp1 backgrounds. Use IP-MS of VRN1 to identify partners and test whether the DNA-binding-dead R249E/R289E/R296E mutant complements vrn1.
Hypothesis: VRN1 is recruited to FLC after cold by interaction with Polycomb maintenance factors.
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