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

Gene ID: 824002, updated on 18-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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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. A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis. Pan J, et al. J Genet Genomics, 2023 Mar. PMID 36113770
  3. The H3K27me3 Demethylase RELATIVE OF EARLY FLOWERING6 Suppresses Seed Dormancy by Inducing Abscisic Acid Catabolism. Chen H, et al. Plant Physiol, 2020 Dec. PMID 33037128, Free PMC Article
  4. DNA methylation repels targeting of Arabidopsis REF6. Qiu Q, et al. Nat Commun, 2019 May 2. PMID 31048693, Free PMC Article
  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 (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  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: Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

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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