SWN (SWINGER; also EZA1, SDG10) is one of three Arabidopsis Enhancer of zeste homologs. It is a SET-domain histone H3K27 methyltransferase and catalytic subunit of Polycomb Repressive Complex 2, acting largely redundantly with CURLY LEAF in sporophytic Polycomb silencing (clf swn double mutants lose H3K27me3 and fail to maintain differentiated identity) and with MEDEA in the female gametophyte. During vernalization, SWN is the E(z) subunit of the cold-formed PHD-PRC2 (with VRN2, FIE, MSI1 and the VEL proteins VIN3, VRN5 and VEL1), which deposits H3K27me3 at the FLC nucleation region. SWN also interacts with HEXOKINASE1 to repress glucose-responsive genes.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003682 chromatin binding | IBA GO_REF:0000033 | ACCEPT | Summary: Chromatin binding inherited in the E(z) family. Propagation Review Root cause: NO FAILURE CORE Sources checked: MGI:MGI:107940 SUPPORTS TRANSFER Ezh2 donor; E(z) proteins act on chromatin. |
| GO:0003727 single-stranded RNA binding | IDA PMID:21127216 Vernalization-mediated epigenetic silencing by a long intron... | KEEP AS NON CORE | Summary: PRC2 (including SWN) was reported to associate with the lncRNA COLDAIR. Reason: Secondary, with a debated role in FLC silencing. Supporting Evidence: PMID:21127216 COLDAIR physically associates with a component of PRC2 and targets PRC2 to FLC. |
| GO:0005515 protein binding | IPI PMID:15456723 Interaction of Polycomb-group proteins controlling flowering... | REMOVE | Summary: Yeast two-hybrid interaction of SWN with VRN2. Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by complex annotations. 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 SWN with VRN2. Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by complex annotations. 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:19452453 Proteomic profiling of tandem affinity purified 14-3-3 prote... | REMOVE | Summary: 14-3-3 (GRF2) high-throughput TAP interactor. Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by complex annotations. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:28428341 Ctf4-related protein recruits LHP1-PRC2 to maintain H3K27me3... | REMOVE | Summary: Interaction with EOL1 (Ctf4-related). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by complex annotations. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:28428341 Ctf4-related protein recruits LHP1-PRC2 to maintain H3K27me3... | REMOVE | Summary: Interaction with EOL1 (Ctf4-related). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by complex annotations. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:29330200 PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 Interacts with Polycomb... | REMOVE | Summary: Interaction with PWO1 (PWWP-domain interactor of Polycombs). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by complex annotations. Removing the generic term does not mean the interaction is false. |
| GO:0005634 nucleus | EXP PMID:35394700 HEXOKINASE1 forms a nuclear complex with the PRC2 subunits C... | ACCEPT | Summary: SWN is nuclear, where it forms a complex with HXK1. Supporting Evidence: PMID:35394700 two catalytic subunits of Polycomb Repressive Complex 2, SWINGER (SWN) and CURLY LEAF (CLF), directly interact with catalytically active HXK1 |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear localization of E(z) proteins. |
| GO:0005634 nucleus | IDA PMID:16924116 Partially redundant functions of two SET-domain polycomb-gro... | ACCEPT | Summary: SWN localizes to nuclei, including in the female gametophyte. Reason: Localization data place SWN with FIS2 and MEA in the female gametophyte. Supporting Evidence: PMID:16924116 Localization data indicated that all three proteins are present in the female gametophyte. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Automated nuclear localization. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP nuclear prediction. |
| GO:0005677 chromatin silencing complex | IDA PMID:18854416 A PHD-polycomb repressive complex 2 triggers the epigenetic ... | ACCEPT | Summary: SWN is the E(z) subunit of the purified cold-formed PHD-PRC2. 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:0006338 chromatin remodeling | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro mapping to chromatin remodeling; broad. |
| GO:0009506 plasmodesma | HDA PMID:21533090 Arabidopsis plasmodesmal proteome. | REMOVE | Summary: SWN was detected in a plasmodesmal proteome from suspension cells. Reason: SWN is a nuclear PRC2 methyltransferase. The study itself reports a large fraction of cytoplasmic contaminants, and no follow-up supports plasmodesmal localization. Supporting Evidence: PMID:21533090 still has a significant number (35%) of putative cytoplasmic contaminants |
| GO:0009737 response to abscisic acid | IGI PMID:30307069 Polycomb repressive complex 2 attenuates ABA-induced senesce... | KEEP AS NON CORE | Summary: clf swn are hypersensitive to ABA-induced senescence. Supporting Evidence: PMID:30307069 suggesting a redundant role for the PRC2 enzymes in negatively regulating ABA-induced senescence. |
| GO:0010048 vernalization response | IMP PMID:16983073 The Arabidopsis thaliana vernalization response requires a p... | ACCEPT | Summary: Vernalization requires PRC2 homologs; SWN is the methyltransferase in PHD-PRC2. Supporting Evidence: PMID:16983073 We demonstrate that the repression of FLC by vernalization requires homologues of other Polycomb Repressive Complex 2 proteins and VRN2. PMID:18854416 The PHD-PRC2 activity increases H3K27me3 throughout the locus to levels sufficient for stable silencing. |
| GO:0031507 heterochromatin formation | IBA GO_REF:0000033 | ACCEPT | Summary: Heterochromatin formation (Polycomb facultative) inherited in the E(z) family. Propagation Review Root cause: NO FAILURE CORE Sources checked: FB:FBgn0000629 SUPPORTS TRANSFER Drosophila E(z) donor. |
| GO:0031519 PcG protein complex | IEA GO_REF:0000002 | ACCEPT | Summary: PcG protein complex; correct. |
| GO:0042054 histone methyltransferase activity | IEA GO_REF:0000002 | ACCEPT | Summary: SET-domain histone methyltransferase; correct. |
| GO:0045814 negative regulation of gene expression, epigenetic | IMP PMID:30307069 Polycomb repressive complex 2 attenuates ABA-induced senesce... | ACCEPT | Summary: SWN with CLF silences senescence genes by H3K27me3. Supporting Evidence: PMID:30307069 suggesting a redundant role for the PRC2 enzymes in negatively regulating ABA-induced senescence. |
| GO:0045892 negative regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: Negative regulation of transcription by E(z) proteins. |
| GO:0046976 histone H3K27 methyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: H3K27 methyltransferase activity inherited from the E(z) family (CLF donor). Propagation Review Root cause: NO FAILURE CORE Sources checked: AGI_LocusCode:AT2G23380 SUPPORTS TRANSFER CLF paralog donor; SWN retains the SET domain and is required for H3K27me3 deposition. Supporting Evidence: PMID:35394700 HXK1 is required for CLF- and SWN-mediated histone H3 lysine 27 (H3K27me3) deposition and glucose-mediated gene repression. |
| GO:0050793 regulation of developmental process | IEA GO_REF:0000117 | ACCEPT | Summary: Regulation of developmental process; broad but correct. |
| GO:0140951 histone H3K27 trimethyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: H3K27 trimethyltransferase activity (Rhea-based); consistent. |
| GO:0141044 epigenetic programming in the endosperm | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Epigenetic programming in the endosperm (ARBA). Reason: SWN acts partly redundantly with MEA in the female gametophyte. Supporting Evidence: PMID:16924116 MEA and SWN perform partially redundant functions in controlling the initiation of endosperm development before fertilization in Arabidopsis. |
| GO:0141044 epigenetic programming in the endosperm | IMP PMID:16527743 Polycomb group complexes self-regulate imprinting of the Pol... | KEEP AS NON CORE | Summary: Vegetative PcG complexes keep MEA silenced. Reason: Abstract-only; we defer to the curator. Supporting Evidence: PMID:16527743 We show that Pc-G complexes maintain MEA transcription silenced throughout vegetative life and male gametogenesis. |
| GO:1900055 regulation of leaf senescence | IGI PMID:30307069 Polycomb repressive complex 2 attenuates ABA-induced senesce... | KEEP AS NON CORE | Summary: clf swn show enhanced ABA-induced leaf senescence. Supporting Evidence: PMID:30307069 suggesting a redundant role for the PRC2 enzymes in negatively regulating ABA-induced senescence. |
| GO:1990110 callus formation | IGI PMID:22927830 Reprogramming of H3K27me3 is critical for acquisition of plu... | KEEP AS NON CORE | Summary: clf swn leaves fail to form callus. Supporting Evidence: PMID:22927830 we found that leaf blades and/or cotyledons of the PRC2 mutants curly leaf swinger (clf swn) and embryonic flower2 (emf2) were defective in callus formation. |
| GO:0035098 ESC/E(Z) complex | IDA PMID:18854416 A PHD-polycomb repressive complex 2 triggers the epigenetic ... | NEW | Summary: SWN is the E(z) catalytic subunit of VRN2-PRC2 in the cold-formed PHD-PRC2. Reason: More specific than chromatin silencing 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. |
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