CLF (CURLY LEAF) is one of three Arabidopsis homologs of Drosophila Enhancer of zeste. It is a SET-domain histone H3 lysine 27 methyltransferase and a catalytic subunit of sporophytic Polycomb Repressive Complex 2, in EMF2-PRC2 and VRN2-PRC2 together with FIE and MSI1. CLF acts partly redundantly with SWINGER to deposit H3K27me3 and silence developmental regulators, including the floral homeotic gene AGAMOUS, class I KNOX genes, FT, FLC and senescence-associated genes. Loss of CLF gives curled leaves and early flowering. During vernalization, CLF is required to spread H3K27me3 from the FLC nucleation region over the whole locus after return to warmth, turning metastable silencing into long-term epigenetic memory.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001222 transcription corepressor binding | IPI PMID:28825728 Cis and trans determinants of epigenetic silencing by Polyco... | MODIFY | Summary: PRE-binding transcription factors recruit PRC2. GOA records CLF binding to the MADS-box TF AGAMOUS (AT4G18960). Reason: The partner given in GOA is a DNA-binding transcription factor, not a corepressor, so DNA-binding transcription factor binding is more accurate. The full text was not available. 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:0003682 chromatin binding | IBA GO_REF:0000033 | ACCEPT | Summary: Chromatin binding inherited in the E(z) family; CLF associates with target chromatin. Propagation Review Root cause: NO FAILURE CORE Sources checked: MGI:MGI:107940 SUPPORTS TRANSFER Ezh2 donor; E(z) proteins act on chromatin across eukaryotes. |
| GO:0003727 single-stranded RNA binding | IDA PMID:21127216 Vernalization-mediated epigenetic silencing by a long intron... | KEEP AS NON CORE | Summary: CLF was reported to bind the vernalization-induced intronic lncRNA COLDAIR in vitro. Reason: The RNA binding is experimentally reported but secondary. Its role in FLC silencing remains debated, and PRC2 RNA binding is promiscuous. Supporting Evidence: PMID:21127216 COLDAIR physically associates with a component of PRC2 and targets PRC2 to FLC. |
| GO:0005515 protein binding | IPI PMID:14871310 FIE and CURLY LEAF polycomb proteins interact in the regulat... | REMOVE | Summary: Interaction of CLF with FIE (ESC homolog; PRC2 core). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:15456723 Interaction of Polycomb-group proteins controlling flowering... | REMOVE | Summary: Interaction of CLF with EMF2 (Su(z)12 homolog; PRC2 core). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:15456723 Interaction of Polycomb-group proteins controlling flowering... | REMOVE | Summary: Interaction of CLF with VRN2 (Su(z)12 homolog; PRC2 core). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:15456723 Interaction of Polycomb-group proteins controlling flowering... | REMOVE | Summary: Interaction of CLF with FIE (PRC2 core). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:16983073 The Arabidopsis thaliana vernalization response requires a p... | REMOVE | Summary: Interaction of CLF with VRN2 (in planta co-purification). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:17881378 The Arabidopsis homologs of trithorax (ATX1) and enhancer of... | REMOVE | Summary: Interaction of CLF with ATX1 (trithorax H3K4 methyltransferase). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but ATX1 is an antagonistic trithorax-group H3K4 methyltransferase rather than a PRC2 subunit or recruiter, and no specific CLF molecular function follows from it. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:18812497 Sexual and apomictic seed formation in Hieracium requires th... | REMOVE | Summary: Interaction of CLF with FIE (Hieracium FIE in vitro). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:19097900 Polycomb silencing of KNOX genes confines shoot stem cell ni... | REMOVE | Summary: Interaction of CLF with RING1A (PRC1 RING protein). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:19452453 Proteomic profiling of tandem affinity purified 14-3-3 prote... | REMOVE | Summary: Interaction of CLF with 14-3-3 GRF2 (high-throughput TAP). Reason: GO:0005515 protein binding is uninformative. This is a high-throughput 14-3-3 TAP interactome hit, without follow-up showing a functional consequence for CLF, and 14-3-3 proteins bind many phosphoproteins. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:21282611 MSI4/FVE interacts with CUL4-DDB1 and a PRC2-like complex to... | REMOVE | Summary: Interaction of CLF with MSI4/FVE. Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:21518870 An E3 ligase complex regulates SET-domain polycomb group pro... | REMOVE | Summary: Interaction of CLF with UCL1 F-box protein. Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but here CLF is the substrate of the UCL1 F-box protein, which targets CLF for degradation; that is a property of UCL1, not a CLF molecular function. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: Interaction of CLF with FIE (CLF IP-MS). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: Interaction of CLF with VRN5 (CLF IP-MS). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: Interaction of CLF with ALP1 (CLF IP-MS). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: Interaction of CLF with VRN2 (CLF IP-MS). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: Interaction of CLF with VEL1 (CLF IP-MS). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: Interaction of CLF with EMF1 (CLF IP-MS). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: Interaction of CLF with LHP1 (CLF IP-MS). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: Interaction of CLF with EMF2 (CLF IP-MS). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: Interaction of CLF with MSI1 (CLF IP-MS). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: Interaction of CLF with ALP1. Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. 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 of CLF with EOL1 (Ctf4-related protein). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. 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 of CLF with EOL1 (Ctf4-related protein). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:41130979 A pair of readers of histone H3K4 methylation recruit Polyco... | REMOVE | Summary: Interaction of CLF with ING2 (H3K4me reader). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:41130979 A pair of readers of histone H3K4 methylation recruit Polyco... | REMOVE | Summary: Interaction of CLF with ING1 (H3K4me reader). Reason: GO:0005515 protein binding is uninformative. The interaction is credible, but PRC2 membership is captured by the complex annotations and recruitment by other factors is a property of those factors. 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: CLF 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:17881378 The Arabidopsis homologs of trithorax (ATX1) and enhancer of... | ACCEPT | Summary: BiFC shows CLF (with ATX1) in the nucleus. Supporting Evidence: PMID:17881378 The yellow signal indicates binding of ATX1 and CLF fusion proteins inside the nucleus |
| GO:0005634 nucleus | IDA PMID:20647345 The CURLY LEAF interacting protein BLISTER controls expressi... | ACCEPT | Summary: CLF colocalizes with BLISTER in the nucleus. Supporting Evidence: PMID:20647345 BLI colocalizes with CLF in the nucleus |
| 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 | IEA GO_REF:0000107 | ACCEPT | Summary: Ortholog-based chromatin silencing complex membership; consistent with CLF in PRC2. 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. |
| GO:0006338 chromatin remodeling | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro mapping to chromatin remodeling; broad, but CLF modifies chromatin. |
| GO:0006355 regulation of DNA-templated transcription | IMP PMID:17881378 The Arabidopsis homologs of trithorax (ATX1) and enhancer of... | ACCEPT | Summary: clf mutants misexpress AGAMOUS and lose H3K27me3 there. Supporting Evidence: PMID:17881378 Disrupted ATX1 or CLF function results in misexpression of AG, recognizable phenotypes and loss of H3K4me3 or H3K27me3 histone H3-tail marks, respectively. |
| GO:0009294 DNA-mediated transformation | IMP PMID:17827277 RNAi-mediated gene silencing reveals involvement of Arabidop... | KEEP AS NON CORE | Summary: An RNAi screen of chromatin genes found reduced Agrobacterium root transformation when SDG1/CLF was silenced. Reason: This is an indirect phenotype from a large-scale RNAi screen, not a core function. Supporting Evidence: PMID:17827277 Silencing of 24 genes resulted in either a weak or strong rat phenotype. |
| GO:0009737 response to abscisic acid | IGI PMID:30307069 Polycomb repressive complex 2 attenuates ABA-induced senesce... | KEEP AS NON CORE | Summary: clf swn double mutants are hypersensitive to ABA-induced senescence. Reason: Downstream consequence of PRC2 silencing of senescence-associated genes. Supporting Evidence: PMID:30307069 suggesting a redundant role for the PRC2 enzymes in negatively regulating ABA-induced senescence. |
| GO:0009909 regulation of flower development | IMP PMID:17881378 The Arabidopsis homologs of trithorax (ATX1) and enhancer of... | ACCEPT | Summary: CLF represses floral homeotic genes and flowering genes (AG, FT). Supporting Evidence: PMID:17881378 Disrupted ATX1 or CLF function results in misexpression of AG, recognizable phenotypes and loss of H3K4me3 or H3K27me3 histone H3-tail marks, respectively. |
| GO:0009965 leaf morphogenesis | IMP PMID:11063708 Genetic analysis of incurvata mutants reveals three independ... | KEEP AS NON CORE | Summary: icu1/clf mutants have curled leaves due to ectopic AG. Reason: This is a pleiotropic phenotype of target de-repression. Supporting Evidence: PMID:11063708 We have shown that icu1 mutations are alleles of the Polycomb group gene CURLY LEAF (CLF) |
| GO:0010048 vernalization response | IMP PMID:16983073 The Arabidopsis thaliana vernalization response requires a p... | ACCEPT | Summary: The vernalization repression of FLC requires PRC2 homologs including CLF/SWN. CLF is needed to spread H3K27me3 for long-term silencing. 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:40858112 can be separated from the stable spread H3K27me3 state in mutants defective in one of the PRC2 methyltransferases genes, CURLY LEAF (CLF) or LIKE HETEROCHROMATIN PROTEIN 1, required to maintain long-term silencing. |
| GO:0010228 vegetative to reproductive phase transition of meristem | IMP PMID:19755537 A single amino acid change in the enhancer of zeste ortholog... | KEEP AS NON CORE | Summary: The gain-of-function clf-59 allele represses FLC and flowers early without vernalization. Reason: Neomorphic allele; it supports CLF acting at FLC but is not a core process role. Supporting Evidence: PMID:19755537 clf-59 mutants have elevated levels of trimethylation on lysine 27 of histone H3 (H3K27me3) at FLC. |
| GO:0031507 heterochromatin formation | IBA GO_REF:0000033 | ACCEPT | Summary: Heterochromatin formation (Polycomb facultative heterochromatin) inherited in the E(z) family. Propagation Review Root cause: NO FAILURE CORE Sources checked: FB:FBgn0000629 SUPPORTS TRANSFER Drosophila E(z) donor; H3K27me3-based silencing is conserved. |
| GO:0031507 heterochromatin formation | IEA GO_REF:0000107 | ACCEPT | Summary: Ortholog-based heterochromatin formation; consistent. |
| GO:0031519 PcG protein complex | IEA GO_REF:0000120 | ACCEPT | Summary: PcG protein complex; correct. 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. |
| GO:0042054 histone methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: SET-domain histone methyltransferase; correct but less specific than H3K27. |
| GO:0045814 negative regulation of gene expression, epigenetic | IMP PMID:30307069 Polycomb repressive complex 2 attenuates ABA-induced senesce... | ACCEPT | Summary: PRC2 enzymes (CLF with SWN) silence ABA-induced senescence genes by H3K27me3. Supporting Evidence: PMID:30307069 suggesting a redundant role for the PRC2 enzymes in negatively regulating ABA-induced senescence. |
| GO:0045815 transcription initiation-coupled chromatin remodeling | IMP PMID:16527743 Polycomb group complexes self-regulate imprinting of the Pol... | MODIFY | Summary: Vegetative PcG complexes keep MEDEA silenced by histone methylation. Reason: Transcription initiation-coupled chromatin remodeling describes remodeling during activation and does not fit Polycomb repression. The supported process is epigenetic silencing. Proposed replacements: negative regulation of gene expression, epigenetic Supporting Evidence: PMID:16527743 We show that Pc-G complexes maintain MEA transcription silenced throughout vegetative life and male gametogenesis. |
| GO:0045892 negative regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: Negative regulation of transcription by E(z) PRC2 subunits. |
| GO:0046976 histone H3K27 methyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: H3K27 methyltransferase activity, the defining E(z) activity; CLF is an experimental donor. Propagation Review Root cause: NO FAILURE CORE Sources checked: AGI_LocusCode:AT2G23380 SUPPORTS TRANSFER CLF itself is among the descendants with experimental support. Supporting Evidence: PMID:17881378 Disrupted ATX1 or CLF function results in misexpression of AG, recognizable phenotypes and loss of H3K4me3 or H3K27me3 histone H3-tail marks, respectively. |
| GO:0046976 histone H3K27 methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: H3K27 methyltransferase activity from ARBA; correct. |
| GO:0048586 regulation of long-day photoperiodism, flowering | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Regulation of long-day photoperiodic flowering, transferred from a rice ortholog. Reason: CLF-PRC2 represses FT (and FLC), and clf mutants flower early in long days, but this is an output of general target silencing. |
| 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 | IMP PMID:17881378 The Arabidopsis homologs of trithorax (ATX1) and enhancer of... | ACCEPT | Summary: clf mutants lose H3K27me3 at AG. Supporting Evidence: PMID:17881378 Disrupted ATX1 or CLF function results in misexpression of AG, recognizable phenotypes and loss of H3K4me3 or H3K27me3 histone H3-tail marks, respectively. |
| GO:0141044 epigenetic programming in the endosperm | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Epigenetic programming in the endosperm (ARBA). Reason: The endosperm E(z) is mainly MEA. CLF contributes to keeping MEA silenced in vegetative tissues. |
| 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, including CLF, maintain MEA silencing. Reason: The paper is abstract-only, so we defer to the curator; this is a secondary role. 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 double mutants show enhanced ABA-induced 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. Reason: Downstream of H3K27me3 reprogramming. 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:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | NEW | Summary: Tagged-CLF IP-MS recovers EMF2, VRN2, MSI1 and FIE: CLF is the E(z) subunit of EMF2-PRC2 and VRN2-PRC2 in vivo. Reason: More specific than PcG protein complex / chromatin silencing complex. 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. |
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