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    REF6 relative of early flowering 6 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 824002, updated on 23-Sep-2024

    Summary

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    Official Symbol
    REF6
    Official Full Name
    relative of early flowering 6
    Primary source
    TAIR:AT3G48430
    Locus tag
    AT3G48430
    See related
    Araport:AT3G48430
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    JMJ12; Jumonji domain-containing protein 12; relative of early flowering 6
    Summary
    Relative of Early Flowering 6 (REF6) encodes a Jumonji N/C and zinc finger domain-containing protein that acts as a positive regulator of flowering in an FLC-dependent pathway. REF6 mutants have hyperacetylation of histone H4 at the FLC locus. REF6 interacts with BES1 in a Y2H assay and in vitro. REF6 may play a role in brassinoteroid signaling by affecting histone methylation in the promoters of BR-responsive genes. It is most closely related to the JHDM3 subfamily of JmjN/C proteins.
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    Genomic context

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    See REF6 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    8
    Sequence:
    Chromosome: 3; NC_003074.8 (17935256..17940792)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene alpha/beta-Hydrolases superfamily protein Neighboring gene Cysteine/Histidine-rich C1 domain family protein Neighboring gene Haloacid dehalogenase-like hydrolase (HAD) superfamily protein Neighboring gene DNAse I-like superfamily protein Neighboring gene Zinc finger C-x8-C-x5-C-x3-H type family protein Neighboring gene RPM1-interacting protein 4 (RIN4) family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The Histone H3K27 Demethylase REF6 Is a Positive Regulator of Light-Initiated Seed Germination in Arabidopsis. Wang Y, et al. Cells, 2023 Jan 12. PMID 36672228, Free PMC Article
    2. Mechanically stimulated TCH3 gene expression in Arabidopsis involves protein phosphorylation and EIN6 downstream of calcium. Wright AJ, et al. Plant Physiol, 2002 Apr. PMID 11950988, Free PMC Article
    3. REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. Cui X, et al. Nat Genet, 2016 Jun. PMID 27111035
    4. REF6 promotes lateral root formation through de-repression of PIN1/3/7 genes. Wang X, et al. J Integr Plant Biol, 2019 Apr. PMID 30267471
    5. The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis. Wang X, et al. PLoS Genet, 2019 Apr. PMID 30969965, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHYTOCHROME-INTERACTING FACTOR 7 and RELATIVE OF EARLY FLOWERING 6 act in shade avoidance memory in Arabidopsis.
      Title: PHYTOCHROME-INTERACTING FACTOR 7 and RELATIVE OF EARLY FLOWERING 6 act in shade avoidance memory in Arabidopsis.
    2. A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis.
      Title: A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis.
    3. The Histone H3K27 Demethylase REF6 Is a Positive Regulator of Light-Initiated Seed Germination in Arabidopsis.
      Title: The Histone H3K27 Demethylase REF6 Is a Positive Regulator of Light-Initiated Seed Germination in Arabidopsis.
    4. Dehydroabietinal promotes flowering time and plant defense in Arabidopsis via the autonomous pathway genes FLOWERING LOCUS D, FVE, and RELATIVE OF EARLY FLOWERING 6.
      Title: Dehydroabietinal promotes flowering time and plant defense in Arabidopsis via the autonomous pathway genes FLOWERING LOCUS D, FVE, and RELATIVE OF EARLY FLOWERING 6.
    5. A new role for histone demethylases in the maintenance of plant genome integrity.
      Title: A new role for histone demethylases in the maintenance of plant genome integrity.
    6. Here the authors identify a chromatin-dependent regulatory mechanism at EIN2 requiring two genes: ETHYLENE-INSENSITIVE6 (EIN6), which is a H3K27me3 demethylase also known as RELATIVE OF EARLY FLOWERING6 (REF6), and EIN6 ENHANCER (EEN), the Arabidopsis homolog of the yeast INO80 chromatin remodeling complex subunit IES6 (INO EIGHTY SUBUNIT).
      Title: Epigenetic silencing of a multifunctional plant stress regulator.
    7. Histone 3 lysine27methylation3 demethylase REF6 promotes lateral root primordium initiation and lateral root emergence.
      Title: REF6 promotes lateral root formation through de-repression of PIN1/3/7 genes.
    8. Study shows that in Arabidopsis non-CG methylation in CTCTGYTY motifs is one way to prevent REF6 targeting. Structural analysis demonstrates that CHG methylation is unfavorable for REF6 binding and attenuates REF6-binding affinity. Results reveal a mechanism for a transcriptional-activating histone-modifying enzyme in avoiding heterochromatic binding through its intrinsic DNA methylation unfavorable DNA-binding activity.
      Title: DNA methylation repels targeting of Arabidopsis REF6.
    9. demonstrate that H3K27me3 REF6 methylation represents an epigenetic mechanism prohibiting the premature transcriptional activation of key developmentally up-regulated senescence regulatory as well as functional genes
      Title: The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis.
    10. Genome-wide analyses showed that REF6 colocalizes with BRM at many genomic sites with the CTCTGYTY motif. Loss of REF6 results in decreased BRM occupancy at BRM-REF6 co-targets
      Title: REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001339369.1
    NM_148863.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables histone H3K27me2/H3K27me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K27me2/H3K27me3 demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_positive_effect abscisic acid catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in epigenetic regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within epigenetic regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in epigenetic regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within ethylene-activated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in heat acclimation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within leaf development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to heterochromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of ethylene-activated signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in regulation of ethylene-activated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within_positive_effect regulation of photoperiodism, flowering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in release of seed from dormancy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to abscisic acid IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within response to brassinosteroid IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to diterpene IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within response to diterpene IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to heat IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to heat IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to mechanical stimulus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within sugar mediated signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within_positive_effect systemic acquired resistance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within unidimensional cell growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within vegetative to reproductive phase transition of meristem IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Ino80 complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    relative of early flowering 6
    NP_680116.2
    • relative of early flowering 6 (REF6); FUNCTIONS IN: sequence-specific DNA binding transcription factor activity, zinc ion binding, nucleic acid binding; INVOLVED IN: in 6 processes; LOCATED IN: nucleus; EXPRESSED IN: 8 plant structures; CONTAINS InterPro DOMAIN/s: Transcription factor jumonji/aspartyl beta-hydroxylase (InterPro:IPR003347), Zinc finger, C2H2-like (InterPro:IPR015880), Transcription factor jumonji (InterPro:IPR013129), Zinc finger, C2H2-type (InterPro:IPR007087), Transcription factor jumonji, JmjN (InterPro:IPR003349), Zinc finger, C2H2-type/integrase, DNA-binding (InterPro:IPR013087); BEST Arabidopsis thaliana protein match is: Zinc finger (C2H2 type) family protein / transcription factor jumonji (jmj) family protein (TAIR:AT5G04240.1); Has 105567 Blast hits to 35250 proteins in 1010 species: Archae - 0; Bacteria - 23; Metazoa - 99094; Fungi - 2247; Plants - 673; Viruses - 7; Other Eukaryotes - 3523 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003074.8 Reference assembly

      Range
      17935256..17940792
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_148863.4 → NP_680116.2  relative of early flowering 6 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_680116.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9STM3
      UniProtKB/TrEMBL
      A0A178VKP4, A0A5S9XJ85
      Conserved Domains (3) summary
      pfam02373
      Location:233 → 352
      JmjC; JmjC domain, hydroxylase
      sd00017
      Location:1268 → 1290
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam02375
      Location:21 → 52
      JmjN; jmjN domain

    2. NM_001339369.1 → NP_001326576.1  relative of early flowering 6 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1I9LPP9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9STM3.1

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