MSI1 (MULTICOPY SUPPRESSOR OF IRA1) is an Arabidopsis WD40-repeat histone-binding protein of the p55/RbAp48 (RBBP4/7) family. It is a shared subunit of several chromatin complexes. MSI1 is present in all plant Polycomb Repressive Complex 2 variants: FIS-PRC2 in the female gametophyte and endosperm, EMF-PRC2 and VRN-PRC2 in the sporophyte, and the cold-formed PHD-PRC2 at FLC. It is required for PRC2-mediated H3K27 trimethylation, repression of seed development before fertilization, and competence to flower after vernalization. MSI1 binds LHP1, linking PRC2 to H3K27me3-marked chromatin in a positive feedback loop. MSI1 is also the p48 subunit of chromatin assembly factor CAF-1 (with FAS1 and FAS2), a component of the RBR1-associated DREAM complex, and a DDB1-binding CUL4 substrate receptor. With RBR1 it represses MET1 during female gametogenesis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001222 transcription corepressor binding | IPI PMID:28825728 Cis and trans determinants of epigenetic silencing by Polyco... | MODIFY | Summary: GOA records MSI1 binding to the MADS-box TF AGAMOUS (AT4G18960) in a study of PRC2 recruitment by PRE-binding TFs. Reason: The partner given in GOA is a DNA-binding TF, not a corepressor. 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:0005515 protein binding | IPI PMID:12970192 Arabidopsis MSI1 is a component of the MEA/FIE Polycomb grou... | REMOVE | Summary: MSI1 interaction with MEA. Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:12970192 Here we show that the Arabidopsis WD-40 domain protein MSI1 is present together with MEA and FIE in a 600 kDa complex and interacts directly with FIE. |
| GO:0005515 protein binding | IPI PMID:12970192 Arabidopsis MSI1 is a component of the MEA/FIE Polycomb grou... | REMOVE | Summary: MSI1 interacts directly with FIE. Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:12970192 Here we show that the Arabidopsis WD-40 domain protein MSI1 is present together with MEA and FIE in a 600 kDa complex and interacts directly with FIE. |
| GO:0005515 protein binding | IPI PMID:18281509 EMBRYONIC FLOWER1 participates in polycomb group-mediated AG... | REMOVE | Summary: MSI1 interaction with EMF1. Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:18281509 EMF1 interaction with MSI1 could indicate that EMF1 is a component of the putative EMF2 complex. |
| GO:0005515 protein binding | IPI PMID:18700816 Retinoblastoma and its binding partner MSI1 control imprinti... | REMOVE | Summary: MSI1 interaction with RBR1. Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. 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: MSI1 interaction with (Hieracium) FIE. Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:21240189 The Arabidopsis CUL4-DDB1 complex interacts with MSI1 and is... | REMOVE | Summary: MSI1 interacts with DDB1A. Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:21240189 Here, we provide evidence that Arabidopsis MSI1 physically interacts with DDB1A and is part of a multimeric protein complex including CUL4. |
| GO:0005515 protein binding | IPI PMID:23778966 Arabidopsis MSI1 connects LHP1 to PRC2 complexes. | REMOVE | Summary: MSI1 interaction with EMF2. Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:23778966 This work established the fact that all known plant PRC2 complexes contain MSI1, a homologue of Drosophila p55. |
| GO:0005515 protein binding | IPI PMID:23778966 Arabidopsis MSI1 connects LHP1 to PRC2 complexes. | MODIFY | Summary: MSI1 binds LHP1, linking PRC2 to an H3K27me3-binding protein. Reason: The paper shows that MSI1 acts as the bridge between PRC2 and LHP1, forming a positive feedback loop that recruits PRC2 to H3K27me3 chromatin. Protein-macromolecule adaptor activity captures this better than protein binding. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:23778966 We found that MSI1 serves to link PRC2 to LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), a protein that binds H3K27me3 in vitro and in vivo and is required for a functional plant PcG system. |
| GO:0005515 protein binding | IPI PMID:23778966 Arabidopsis MSI1 connects LHP1 to PRC2 complexes. | REMOVE | Summary: MSI1 interaction with FIE. Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:23778966 This work established the fact that all known plant PRC2 complexes contain MSI1, a homologue of Drosophila p55. |
| GO:0005515 protein binding | IPI PMID:26642436 Kicking against the PRCs - A Domesticated Transposase Antago... | REMOVE | Summary: MSI1 co-purification with ALP1. Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. Removing the generic term does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:34583930 The DREAM complex represses growth in response to DNA damage... | REMOVE | Summary: MSI1 in RBR1/DREAM complexes (interaction with an E2F). Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:34583930 In addition to the previously described DREAM components these complexes also included the RBBP4 homolog MSI1 |
| GO:0005515 protein binding | IPI PMID:37072400 A VEL3 histone deacetylase complex establishes a maternal ep... | REMOVE | Summary: MSI1 interacts with VEL3. Reason: GO:0005515 protein binding is uninformative. MSI1 is a shared WD40 histone-binding subunit of PRC2, CAF-1 and other chromatin complexes. These complex memberships are captured by complex annotations. Removing the generic term does not mean the interaction is false. Supporting Evidence: PMID:37072400 VEL3 interacts with MSI1 and can direct MSI1 to the nucleolus. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear localization of RbAp48/p55-family proteins. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt nuclear localization. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP nuclear prediction. |
| GO:0005634 nucleus | TAS PMID:12736201 Arabidopsis MSI1 is required for epigenetic maintenance of r... | ACCEPT | Summary: MSI1 is a nuclear chromatin protein. |
| GO:0005677 chromatin silencing complex | IDA PMID:18854416 A PHD-polycomb repressive complex 2 triggers the epigenetic ... | ACCEPT | Summary: MSI1 is a core subunit of purified 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 | IBA GO_REF:0000033 | ACCEPT | Summary: Chromatin remodeling for the p55/RbAp48 family (chromatin assembly and modification complexes). Propagation Review Root cause: NO FAILURE CORE Sources checked: AGI_LocusCode:AT2G19520 SUPPORTS TRANSFER MSI4/FVE paralog donor; MSI proteins act in chromatin-modifying complexes. |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: Regulation of transcription for the p55 family. Propagation Review Root cause: NO FAILURE CORE Sources checked: AGI_LocusCode:AT2G19520 SUPPORTS TRANSFER MSI4/FVE donor. |
| GO:0009555 pollen development | IGI PMID:18045841 Chromatin assembly factor 1 regulates the cell cycle but not... | KEEP AS NON CORE | Summary: Loss of CAF-1 (FAS1/MSI1) causes cell-cycle delay in pollen development. Supporting Evidence: PMID:18045841 loss of activity of the Chromatin assembly factor 1 (CAF1) pathway causes delay and arrest of the cell cycle during pollen development. |
| GO:0009555 pollen development | IMP PMID:18045841 Chromatin assembly factor 1 regulates the cell cycle but not... | KEEP AS NON CORE | Summary: CAF-1 deficiency delays pollen mitosis. Supporting Evidence: PMID:18045841 loss of activity of the Chromatin assembly factor 1 (CAF1) pathway causes delay and arrest of the cell cycle during pollen development. |
| GO:0009555 pollen development | IMP PMID:19237690 A collection of Ds insertional mutants associated with defec... | KEEP AS NON CORE | Summary: Male gametophyte transmission defect in a Ds insertion screen. Reason: Large-scale screen; pleiotropic. |
| GO:0009793 embryo development ending in seed dormancy | IMP PMID:15634699 Genetic and molecular identification of genes required for f... | KEEP AS NON CORE | Summary: Maternal-effect seed defect in a female gametophyte Ds screen. Reason: Consistent with the FIS-PRC2 role; large-scale screen. |
| GO:0009909 regulation of flower development | IMP PMID:16554362 Regulation of flowering time by Arabidopsis MSI1. | KEEP AS NON CORE | Summary: msi1 partial mutants flower late; MSI1 is needed for active marks at SOC1. Supporting Evidence: PMID:16554362 MSI1 is needed to establish epigenetic H3K4 di-methylation and H3K9 acetylation marks in SOC1 chromatin. |
| GO:0010026 trichome differentiation | IMP PMID:17021044 Chromatin assembly factor CAF-1 is required for cellular dif... | KEEP AS NON CORE | Summary: CAF-1 mutants show altered trichome branching. Supporting Evidence: PMID:17021044 Biochemical evidence suggests that FASCIATA1, FASCIATA2 and MSI1 form CAF-1 in Arabidopsis thaliana. |
| GO:0010214 seed coat development | IMP PMID:17172356 The female gametophyte and the endosperm control cell prolif... | KEEP AS NON CORE | Summary: msi1 autonomous seeds develop seed coat without fertilization. Supporting Evidence: PMID:17172356 Cell proliferation and differentiation of the seed coat occur in autonomous seeds produced in the absence of fertilization of the multicopy suppressor of ira1 (msi1) mutant. |
| GO:0016480 negative regulation of transcription by RNA polymerase III | IPI PMID:18700816 Retinoblastoma and its binding partner MSI1 control imprinti... | MODIFY | Summary: MSI1 with RBR1 directly represses MET1 transcription during female gametogenesis. Reason: MET1 is a protein-coding RNA polymerase II gene, so RNA polymerase III is the wrong target class. Proposed replacements: negative regulation of transcription by RNA polymerase II Supporting Evidence: PMID:18700816 This Rb-dependent activation is mediated by direct transcriptional repression of MET1 during female gametogenesis. |
| GO:0031507 heterochromatin formation | IMP PMID:16452472 Functional genomic analysis of CAF-1 mutants in Arabidopsis ... | KEEP AS NON CORE | Summary: CAF-1 mutants have reduced cytological heterochromatin. Reason: Via CAF-1 chromatin assembly. Supporting Evidence: PMID:16452472 These results suggest that CAF-1 functions in heterochromatin formation. |
| GO:0032991 protein-containing complex | IPI PMID:12970192 Arabidopsis MSI1 is a component of the MEA/FIE Polycomb grou... | MODIFY | Summary: MSI1 is in a 600 kDa complex with MEA and FIE. Reason: The complex is FIS-PRC2, so ESC/E(Z) complex is the specific term. Proposed replacements: ESC/E(Z) complex Supporting Evidence: PMID:12970192 Here we show that the Arabidopsis WD-40 domain protein MSI1 is present together with MEA and FIE in a 600 kDa complex and interacts directly with FIE. |
| GO:0042393 histone binding | IBA GO_REF:0000033 | ACCEPT | Summary: Histone binding by the p55/RbAp48 WD40 propeller. Propagation Review Root cause: NO FAILURE CORE Sources checked: FB:FBgn0263979 SUPPORTS TRANSFER Drosophila Caf1-55 donor; histone H3/H4 binding is conserved. |
| GO:0045787 positive regulation of cell cycle | IGI PMID:18045841 Chromatin assembly factor 1 regulates the cell cycle but not... | KEEP AS NON CORE | Summary: CAF-1 promotes cell-cycle progression in pollen. Supporting Evidence: PMID:18045841 loss of activity of the Chromatin assembly factor 1 (CAF1) pathway causes delay and arrest of the cell cycle during pollen development. |
| GO:0048316 seed development | IMP PMID:17172356 The female gametophyte and the endosperm control cell prolif... | KEEP AS NON CORE | Summary: msi1 seeds abort maternally and form autonomous seeds. Supporting Evidence: PMID:17172356 Cell proliferation and differentiation of the seed coat occur in autonomous seeds produced in the absence of fertilization of the multicopy suppressor of ira1 (msi1) mutant. |
| GO:0048366 leaf development | IMP PMID:17021044 Chromatin assembly factor CAF-1 is required for cellular dif... | KEEP AS NON CORE | Summary: CAF-1 mutants have altered leaf size. Supporting Evidence: PMID:17021044 Biochemical evidence suggests that FASCIATA1, FASCIATA2 and MSI1 form CAF-1 in Arabidopsis thaliana. |
| GO:0070176 DRM complex | IDA PMID:32661276 DREAM complex suppresses DNA methylation maintenance genes a... | KEEP AS NON CORE | Summary: MSI1 is a component of the plant DREAM (DRM) complex with RBR1, E2Fs and LIN proteins. Reason: Supported by independent purifications; this is a non-PRC2 role of MSI1. Supporting Evidence: PMID:34583930 In addition to the previously described DREAM components these complexes also included the RBBP4 homolog MSI1 |
| GO:0070828 heterochromatin organization | IMP PMID:12736201 Arabidopsis MSI1 is required for epigenetic maintenance of r... | KEEP AS NON CORE | Summary: MSI1 reduction alters chromatin and homeotic gene expression. Supporting Evidence: PMID:12736201 AtMSI1 is required to maintain the correct temporal and organ-specific expression of homeotic genes |
| GO:0080008 Cul4-RING E3 ubiquitin ligase complex | ISS PMID:18223036 Characterization of Arabidopsis and rice DWD proteins and th... | KEEP AS NON CORE | Summary: MSI1 has a DWD motif predicted to bind DDB1, and it interacts with DDB1A in a CUL4 complex. Reason: Experimentally supported by Dumbliauskas et al. 2011; this is a secondary role. Supporting Evidence: PMID:21240189 Here, we provide evidence that Arabidopsis MSI1 physically interacts with DDB1A and is part of a multimeric protein complex including CUL4. |
| GO:0045814 negative regulation of gene expression, epigenetic | IMP PMID:23778966 Arabidopsis MSI1 connects LHP1 to PRC2 complexes. | NEW | Summary: MSI1 is required for PRC2 H3K27me3 deposition and target gene repression by EMF- and VRN-PRC2. Reason: MSI1 is a PRC2 core subunit that does part of the silencing work (histone binding and LHP1 bridging). Supporting Evidence: PMID:23778966 plant MSI1 was required for the functions of the EMBRYONIC FLOWER and the VERNALIZATION PRC2 complexes including trimethylation of histone H3 Lys27 (H3K27) at the target chromatin, as well as gene repression and establishment of competence to flower. |
| GO:0035098 ESC/E(Z) complex | IDA PMID:23778966 Arabidopsis MSI1 connects LHP1 to PRC2 complexes. | NEW | Summary: MSI1 is present in all known plant PRC2 complexes (FIS, EMF and VRN). Reason: Core complex membership. Supporting Evidence: PMID:23778966 This work established the fact that all known plant PRC2 complexes contain MSI1, a homologue of Drosophila p55. |
| GO:0033186 CAF-1 complex | TAS PMID:17021044 Chromatin assembly factor CAF-1 is required for cellular dif... | NEW | Summary: MSI1 forms CAF-1 with FAS1 and FAS2. Reason: This is the established second complex of MSI1, the p48 subunit of chromatin assembly factor 1. Supporting Evidence: PMID:17021044 Biochemical evidence suggests that FASCIATA1, FASCIATA2 and MSI1 form CAF-1 in Arabidopsis thaliana. |
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