VAL1 (VIVIPAROUS1/ABI3-LIKE 1; also HSI2) is a nuclear B3-domain transcriptional repressor. It combines a B3 DNA-binding domain that recognizes the Sph/RY element (CATGCA), a PHD-like domain implicated in reading H3K27 methylation, a CW-type zinc finger and a C-terminal EAR repression motif. VAL1 binds RY elements in target loci and recruits repressive chromatin machinery, including the Polycomb proteins LHP1/PRC1 and the PRC2 methyltransferases CLF and SWN, as well as the ASAP complex and histone deacetylase activity. Redundantly with VAL2, it represses the seed-maturation program (LEC1, ABI3, FUS3, DOG1) after germination, and during vernalization it binds two RY elements in the FLC intragenic nucleation region to trigger Polycomb (PHD-PRC2) nucleation and epigenetic silencing of FLC.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for transcription cis-regulatory region binding in the VAL B3 clade. Reason: The VAL1 B3 domain binds the Sph/RY element (CATGCA) found in cis-regulatory regions such as the FLC nucleation region and seed-maturation gene promoters; supported by crystal structure and EMSA. Supporting Evidence: PMID:29660015 crystal structure of VAL1 B3 domain (VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA sequence |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO DNA binding from the B3 domain. Reason: Correct but general; the B3 domain of VAL1 binds a specific Sph/RY sequence, so sequence-specific DNA binding is more informative. Proposed replacements: sequence-specific DNA binding Supporting Evidence: PMID:29660015 crystal structure of VAL1 B3 domain (VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA sequence |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: Genome-wide classification of Arabidopsis transcription factors placed VAL1 among B3-domain DNA-binding transcription factors (ISS). Reason: VAL1 is an active B3/EAR transcriptional repressor; DNA-binding transcription repressor activity is the more precise child term. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:15894743 These results indicate that HSI2 and related proteins are B3 domain-EAR motif active transcription repressors. |
| GO:0005515 protein binding | IPI PMID:19962994 PAH-domain-specific interactions of the Arabidopsis transcri... | MODIFY | Summary: VAL1/HSI2 recorded as a yeast two-hybrid partner of the SIN3-like corepressor SNL1. Reason: The abstract does not name HSI2/VAL1 but the curator saw the full interaction list; deferring on the interaction. Binding of an EAR-motif repressor to a SIN3-like HDAC-associated corepressor is best described as transcription corepressor binding. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:19962994 full-length SNL1 was shown to repress transcription in a histone-deacetylase-dependent manner |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: Binary Y2H interaction with the ABA receptor PYL9 from a phytohormone interactome screen. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. This is an unvalidated systematic pair with no functional characterization for VAL1. Supporting Evidence: PMID:32612234 consisting of more than 2,000 binary protein-protein interactions |
| GO:0005515 protein binding | IPI PMID:33270882 The transcriptional repressors VAL1 and VAL2 recruit PRC2 fo... | REMOVE | Summary: VAL1 interacts in vivo with the PRC2 catalytic subunit CLF. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. The functional content (VAL1 recruits PRC2 to RY-containing targets) is captured in core_functions; no GO MF term for PRC2 binding exists. Supporting Evidence: PMID:33270882 We further show that VAL1 and VAL2 physically interact with SWN and CLF in vivo. |
| GO:0005515 protein binding | IPI PMID:33270882 The transcriptional repressors VAL1 and VAL2 recruit PRC2 fo... | REMOVE | Summary: VAL1 interacts in vivo with the PRC2 catalytic subunit SWN. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. The functional content (VAL1 recruits PRC2 to RY-containing targets) is captured in core_functions; no GO MF term for PRC2 binding exists. Supporting Evidence: PMID:33270882 We further show that VAL1 and VAL2 physically interact with SWN and CLF in vivo. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear localization by phylogenetic/electronic inference, consistent with experimental data. Reason: VAL1 is a nuclear DNA-binding repressor. Supporting Evidence: file:ARATH/VAL1/VAL1-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005634 nucleus | IDA PMID:15894743 Analysis of a sugar response mutant of Arabidopsis identifie... | ACCEPT | Summary: HSI2/VAL1 fusion protein is targeted to the nucleus; C-terminal deletion reduces nuclear targeting. Reason: Direct experimental evidence of nuclear localization. Supporting Evidence: PMID:15894743 Deletion of the C-terminal portion of HSI2 lost in the hsi2 mutant caused reduced nuclear targeting of HSI2. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Nuclear localization by phylogenetic/electronic inference, consistent with experimental data. Reason: VAL1 is a nuclear DNA-binding repressor. Supporting Evidence: file:ARATH/VAL1/VAL1-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: Nuclear localization by phylogenetic/electronic inference, consistent with experimental data. Reason: VAL1 is a nuclear DNA-binding repressor. Supporting Evidence: file:ARATH/VAL1/VAL1-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005739 mitochondrion | HDA PMID:14671022 Experimental analysis of the Arabidopsis mitochondrial prote... | MARK AS OVER ANNOTATED | Summary: Detection in a large LC-MS/MS mitochondrial proteome. Reason: VAL1 is a nuclear B3 transcriptional repressor with no mitochondrial targeting signal or mitochondrial function; the authors note that many identified proteins lack mitochondrial targeting prediction. A single proteomic detection is most likely co-purification; kept only as an over-annotation rather than removed because it is an experimental (HDA) row. Supporting Evidence: PMID:14671022 Only approximately half of the experimental set is predicted to be mitochondrial by targeting prediction programs |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000117 | MODIFY | Summary: ARBA-based regulation of DNA-templated transcription. Reason: VAL1 is an active repressor; the negative regulation term is more accurate. Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:15894743 These results indicate that HSI2 and related proteins are B3 domain-EAR motif active transcription repressors. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO zinc ion binding from the CW-type zinc finger. Reason: VAL1 contains CW and PHD-like zinc-finger modules that structurally bind zinc; correct but not an informative core function. Supporting Evidence: file:ARATH/VAL1/VAL1-uniprot.txt CW-type |
| GO:0009737 response to abscisic acid | TAS PMID:15894743 Analysis of a sugar response mutant of Arabidopsis identifie... | KEEP AS NON CORE | Summary: hsi2/val1 mutant phenotypes in seed-maturation gene repression were discussed with respect to ABA. Reason: VAL1 represses ABA-related seed maturation regulators (ABI3, DOG1), so ABA responses are an indirect, downstream context. The cached abstract notes the hsi2 sugar phenotype is not due to elevated ABA; full text not seen, deferring to the TAS curator but keeping as non-core. Supporting Evidence: PMID:15894743 which was not due to increased level of abscisic acid |
| GO:0009744 response to sucrose | TAS PMID:15894743 Analysis of a sugar response mutant of Arabidopsis identifie... | KEEP AS NON CORE | Summary: hsi2 mutants show enhanced expression of a sugar-inducible reporter under low- and high-sugar conditions. Reason: Derepression of a sugar-inducible seed-maturation reporter is a downstream consequence of loss of VAL1 repression; non-core. Supporting Evidence: PMID:15894743 caused enhanced LUC expression under both low- and high-sugar conditions |
| GO:0045892 negative regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for negative regulation of transcription in the VAL clade. Reason: Core process for an EAR-motif B3 repressor; experimentally supported for VAL1. Supporting Evidence: PMID:15894743 These results indicate that HSI2 and related proteins are B3 domain-EAR motif active transcription repressors. |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:15894743 Analysis of a sugar response mutant of Arabidopsis identifie... | ACCEPT | Summary: HSI2/VAL1 overexpression and transient expression repressed reporter expression, dependent on the EAR motif. Reason: Direct experimental evidence of active transcriptional repression. Supporting Evidence: PMID:15894743 Transient coexpression of 35SHSI2 with Spo(min)LUC in protoplasts repressed the expression of LUC activity |
| GO:0043565 sequence-specific DNA binding | IDA PMID:29660015 Structural basis of DNA target recognition by the B3 domain ... | NEW | Summary: NEW annotation. The VAL1 B3 domain was crystallized bound to the Sph/RY element and its binding specificity measured by EMSA competition. Reason: Direct structural and biochemical demonstration of sequence-specific DNA binding by VAL1; this is the activity by which VAL1 targets the FLC nucleation region. Supporting Evidence: PMID:29660015 crystal structure of VAL1 B3 domain (VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA sequence PMID:29660015 allowed us to determine the relative affinities of VAL1-B3 to various recognition sequence variants |
| GO:0010048 vernalization response | IMP PMID:27471304 Arabidopsis transcriptional repressor VAL1 triggers Polycomb... | NEW | Summary: NEW annotation. A point mutation in the FLC nucleation-region RY element and VAL1 loss block cold-induced PHD-PRC2 nucleation; VAL1 binds the nucleation region in vivo and promotes deacetylation and silencing. Reason: VAL1 performs a step of the process itself: it binds the cold memory element and recruits/positions the silencing machinery (LHP1/PRC1, ASAP, PRC2) for nucleation. Two independent studies support this. This is participation, not merely necessity. Supporting Evidence: PMID:27471304 VAL1 localizes to the nucleation region in vivo, promoting histone deacetylation and FLC transcriptional silencing PMID:27819666 two homologous trans-acting epigenome readers, VAL1 and VAL2, control vernalization-mediated FLC silencing |
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Download this section (compressed HTML)Q: Does the VAL1 PHD-like domain directly read H3K27me3 in vivo at FLC, and is this reading required for maintenance or only nucleation of silencing?
Experiment: Complement val1 with B3 DNA-binding-dead (structure-guided), PHD-L and EAR-motif mutants and measure FLC nucleation-region H3K27me3 and H2Aub during and after cold, separating DNA targeting from co-repressor recruitment.
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