VIN3_ARATH
ID VIN3_ARATH Reviewed; 620 AA.
AC Q9FIE3; Q53YX0;
DT 02-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 12-JUN-2007, sequence version 2.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=Protein VERNALIZATION INSENSITIVE 3;
GN Name=VIN3; OrderedLocusNames=At5g57380; ORFNames=MSF19.4;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, TISSUE
RP SPECIFICITY, AND INDUCTION.
RC STRAIN=cv. Columbia;
RX PubMed=14712276; DOI=10.1038/nature02195;
RA Sung S., Amasino R.M.;
RT "Vernalization in Arabidopsis thaliana is mediated by the PHD finger
RT protein VIN3.";
RL Nature 427:159-164(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10048488; DOI=10.1093/dnares/5.6.379;
RA Asamizu E., Sato S., Kaneko T., Nakamura Y., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence
RT features of the regions of 1,081,958 bp covered by seventeen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:379-391(1998).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH VIL1 AND VIL2, AND
RP INDUCTION BY COLD.
RC STRAIN=cv. Columbia;
RX PubMed=17114575; DOI=10.1101/gad.1493306;
RA Sung S., Schmitz R.J., Amasino R.M.;
RT "A PHD finger protein involved in both the vernalization and photoperiod
RT pathways in Arabidopsis.";
RL Genes Dev. 20:3244-3248(2006).
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, INDUCTION BY COLD, INTERACTION WITH VIL1,
RP AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17174094; DOI=10.1016/j.cub.2006.11.052;
RA Greb T., Mylne J.S., Crevillen P., Geraldo N., An H., Gendall A.R.,
RA Dean C.;
RT "The PHD finger protein VRN5 functions in the epigenetic silencing of
RT Arabidopsis FLC.";
RL Curr. Biol. 17:73-78(2007).
RN [6]
RP SUBUNIT, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=18854416; DOI=10.1073/pnas.0808687105;
RA De Lucia F., Crevillen P., Jones A.M.E., Greb T., Dean C.;
RT "A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of
RT FLC during vernalization.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:16831-16836(2008).
CC -!- FUNCTION: Plays a central role in vernalization by mediating the
CC initial transcriptional repression of the homeotic gene FLC, a floral
CC repressor, after a cold treatment. However, due to its transient
CC expression, it cannot maintain repression of FLC, which is then
CC maintained by Polycomb Group complexes containing VRN2 throughout
CC development. Required to deacetylate histones on the FLC promoter.
CC Together with VIL1, required during vernalization for the modifications
CC of FLC and FLM chromatin that are associated with an epigenetically
CC silenced state (e.g. chromatin modifications, histone deacetylation,
CC and trimethylated H3 'Lys-4' H3K4me3 and 'Lys-27' H3K27me3) and with
CC acquisition of competence to flower. {ECO:0000269|PubMed:14712276,
CC ECO:0000269|PubMed:17114575, ECO:0000269|PubMed:17174094}.
CC -!- SUBUNIT: Interacts with VIL1 and VIL2. The heterodimer made of VIN3 and
CC VIL1 is required for establishing the vernalization-induced epigenetic
CC silencing of FLC. Component of the plant homeodomain / polycomb
CC repressive complex 2 (PHD-PRC2) large complex during prolonged cold,
CC composed of core PRC2 components (VRN2, EZA1, FIE and MSI1), and three
CC related PHD finger proteins (VIL1, VIL2 and VIN3) that mediates histone
CC H3 trimethylation on 'Lys-27' (H3K27me3). {ECO:0000269|PubMed:17114575,
CC ECO:0000269|PubMed:17174094, ECO:0000269|PubMed:18854416}.
CC -!- INTERACTION:
CC Q9FIE3; Q8W5B1: VRN2; NbExp=2; IntAct=EBI-2358223, EBI-2128880;
CC -!- SUBCELLULAR LOCATION: Nucleus. Nucleus speckle. Note=Probably DNA-
CC associated; interacts directly with the FLC regulatory regions.
CC -!- TISSUE SPECIFICITY: Expressed in shoot and root apices. Displays the
CC same pattern of expression as FLC. {ECO:0000269|PubMed:14712276}.
CC -!- INDUCTION: By cold. Expressed only after a duration of cold exposure
CC that is effective for vernalization. Strongly down-regulated after
CC return to a warm growth temperature. {ECO:0000269|PubMed:14712276,
CC ECO:0000269|PubMed:17114575, ECO:0000269|PubMed:17174094}.
CC -!- DISRUPTION PHENOTYPE: Impaired vernalization response with incomplete
CC repression of FLC during and after cold exposure, due to a reduction in
CC vernalization-induced histone H3 deacetylation and methylation (e.g.
CC H3K4me3 and H3K27me3). {ECO:0000269|PubMed:17114575,
CC ECO:0000269|PubMed:17174094}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB08475.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AY446960; AAR91717.2; -; mRNA.
DR EMBL; AB016891; BAB08475.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED96894.1; -; Genomic_DNA.
DR RefSeq; NP_001332646.1; NM_001345260.1.
DR RefSeq; NP_200548.2; NM_125121.3.
DR AlphaFoldDB; Q9FIE3; -.
DR BioGRID; 21088; 3.
DR DIP; DIP-48611N; -.
DR IntAct; Q9FIE3; 3.
DR STRING; 3702.AT5G57380.1; -.
DR PaxDb; Q9FIE3; -.
DR PRIDE; Q9FIE3; -.
DR EnsemblPlants; AT5G57380.1; AT5G57380.1; AT5G57380.
DR GeneID; 835844; -.
DR Gramene; AT5G57380.1; AT5G57380.1; AT5G57380.
DR KEGG; ath:AT5G57380; -.
DR Araport; AT5G57380; -.
DR TAIR; locus:2173004; AT5G57380.
DR eggNOG; ENOG502QR8D; Eukaryota.
DR HOGENOM; CLU_016873_0_0_1; -.
DR InParanoid; Q9FIE3; -.
DR OMA; EQERYGI; -.
DR OrthoDB; 191691at2759; -.
DR PhylomeDB; Q9FIE3; -.
DR PRO; PR:Q9FIE3; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FIE3; baseline and differential.
DR GO; GO:0005677; C:chromatin silencing complex; IDA:UniProtKB.
DR GO; GO:0016607; C:nuclear speck; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0070417; P:cellular response to cold; IEP:UniProtKB.
DR GO; GO:0045814; P:negative regulation of gene expression, epigenetic; IMP:UniProtKB.
DR GO; GO:0061087; P:positive regulation of histone H3-K27 methylation; IMP:UniProtKB.
DR GO; GO:0051571; P:positive regulation of histone H3-K4 methylation; IMP:UniProtKB.
DR GO; GO:0009409; P:response to cold; IEP:UniProtKB.
DR GO; GO:0001666; P:response to hypoxia; IMP:TAIR.
DR GO; GO:0010048; P:vernalization response; IMP:UniProtKB.
DR CDD; cd00063; FN3; 1.
DR Gene3D; 2.60.40.10; -; 1.
DR InterPro; IPR003961; FN3_dom.
DR InterPro; IPR036116; FN3_sf.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR032881; Oberon_PHD.
DR InterPro; IPR044514; VIN3-like.
DR PANTHER; PTHR46286; PTHR46286; 1.
DR Pfam; PF00041; fn3; 1.
DR Pfam; PF07227; PHD_Oberon; 1.
DR SUPFAM; SSF49265; SSF49265; 1.
DR PROSITE; PS50853; FN3; 1.
PE 1: Evidence at protein level;
KW DNA-binding; Metal-binding; Nucleus; Reference proteome; Repressor;
KW Stress response; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..620
FT /note="Protein VERNALIZATION INSENSITIVE 3"
FT /id="PRO_0000059334"
FT DOMAIN 314..412
FT /note="Fibronectin type-III"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00316"
FT ZN_FING 148..206
FT /note="PHD-type"
FT REGION 411..466
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 512..620
FT /note="VIN3-Interacting Domain (VID)"
FT /evidence="ECO:0000250"
FT MOTIF 213..220
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000250"
FT MOTIF 493..500
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000250"
FT COMPBIAS 418..451
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 452..466
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 620 AA; 69347 MW; C145D4E88D3BD588 CRC64;
MQAASLSKIW RFDGNVGPEN MDSSSFEDNE CIETCKPNVL NVSERRELIH ALSNQPEEAS
ELLNSWSRNE IMKIICAEMG KERKYTGLNK PKLIENLLNL VSRPLGETSC SDRRNSRKKE
KKMIGYIICC ENLACRAALG CDDTFCRRCS CCICQKFDDN KDPSLWLTCD ACGSSCHLEC
GLKQDRYGIG SDDLDGRFYC AYCGKDNDLL GCWRKQVKVA KETRRVDVLC YRLSLGQKLL
RGTTKYRNLL ELMDEAVKKL EGDVGPLSGW AMKMARGIVN RLSSGVHVQK LCSQAMEALD
KVVSPSESVS GQGDKMTVRV EEIQARSVTV RVDSEEPSSS TQNKITGFRL FCRKSKDEEC
SSQGNCVVYL PETTSAIQGL EPDTEFCLRV VSFNEEGDLD ESELRFTTLK DDGDEAGDQQ
SPLTNSSSGL CSNPSLPEDE SNNVNKSCSK GNGDKDNTEH CSAGEVESEL EEERLVKRKA
NKIDGRDLLV TPCKRDIYKG KQGGNKRFKS RTVSLNEKPE INNAANGVGD KDLGHIVKTI
RCLEEEGHID KSFRERFLTW YSLRATHREV RVVKIFVETF MEDLSSLGQQ LVDTFSESIL
SKRSSTNGVV PAGICLKLWH
