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    SUVH4 histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4-like protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 831244, updated on 18-Sep-2024

    Summary

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    Official Symbol
    SUVH4
    Official Full Name
    histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4-like protein
    Primary source
    TAIR:AT5G13960
    Locus tag
    AT5G13960
    See related
    Araport:AT5G13960
    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
    KRYPTONITE; KYP; MAC12.7; MAC12_7; SDG33; SET DOMAIN PROTEIN 33; SU(VAR)3-9 homolog 4
    Summary
    Encodes a histone 3 lysine 9 specific methyltransferase involved in the maintenance of DNA methylation. SUVH4/KYP is a SU(VAR)3-9 homolog, a SET domain protein. Known SET domain proteins are involved in epigenetic control of gene expression. There are 10 SUVH genes in Arabidopsis and members of this subfamily of the SET proteins have an additional conserved SRA domain. In kyp mutants, there is a loss of CpNpG methylation. The protein was shown to bind to methylated cytosines of CG, CNG and CNN motifs via its SRA domain but has a preference for the latter two. There is also evidence that KYP/SUVH4 might be involved in the telomerase-independent process known as Alternative Lengthening of Telomeres.
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    Genomic context

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    See SUVH4 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    14
    Sequence:
    Chromosome: 5; NC_003076.8 (4501362..4506250)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene aminopeptidase Neighboring gene Chalcone and stilbene synthase family protein Neighboring gene ncRNA Neighboring gene nuclear factor kappa-B-binding protein Neighboring gene midasin-like protein Neighboring gene Glycosyl hydrolase family 38 protein Neighboring gene exocyst subunit exo70 family protein C2 Neighboring gene NAC domain containing protein 84

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense. Castillo-González C, et al. Elife, 2015 Sep 7. PMID 26344546, Free PMC Article
    2. A novel role for histone methyltransferase KYP/SUVH4 in the control of Arabidopsis primary seed dormancy. Zheng J, et al. New Phytol, 2012 Feb. PMID 22122546
    3. Mechanism of DNA methylation-directed histone methylation by KRYPTONITE. Du J, et al. Mol Cell, 2014 Aug 7. PMID 25018018, Free PMC Article
    4. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Ebbs ML, et al. Mol Cell Biol, 2005 Dec. PMID 16287862, Free PMC Article
    5. Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2. Hung FY, et al. Commun Biol, 2023 Feb 24. PMID 36828846, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2.
      Title: Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2.
    2. CMT3-SUVH4 is the major pathway controlling silencing of the exonic Evelknievel retroelement via inducing non-CG methylation.
      Title: CMT3 and SUVH4/KYP silence the exonic Evelknievel retroelement to allow for reconstitution of CMT1 mRNA.
    3. the histone deacetylase HDA6 can interact with the histone methyltransferases SUVH4, SUVH5, and SUVH6 (SUVH4/5/6).
      Title: HISTONE DEACETYLASE6 Acts in Concert with Histone Methyltransferases SUVH4, SUVH5, and SUVH6 to Regulate Transposon Silencing.
    4. The authors conclude that geminivirus TrAP attenuates the transcriptional gene silencing of the viral chromatin by inhibiting KYP activity to evade host surveillance.
      Title: Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense.
    5. The structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation.
      Title: Mechanism of DNA methylation-directed histone methylation by KRYPTONITE.
    6. Genetic analysis showed that DOG1 and HUB1 are epistatic to KYP/SUVH4, suggesting that these genes regulate seed dormancy in the same genetic pathway.
      Title: A novel role for histone methyltransferase KYP/SUVH4 in the control of Arabidopsis primary seed dormancy.
    7. H3 lysine 9 methylation epigenetic modifications are reduced in an suvh4 suvh6 double mutant
      Title: H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_121399.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables double-stranded methylated DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyl-CpG binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methyl-CpNpG binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methyl-CpNpN binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within peptidyl-lysine methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4-like protein
    NP_196900.1
    • SU(VAR)3-9 homolog 4 (SUVH4); FUNCTIONS IN: double-stranded methylated DNA binding, methyl-CpNpG binding, methyl-CpG binding, histone methyltransferase activity (H3-K9 specific), methyl-CpNpN binding; INVOLVED IN: maintenance of DNA methylation, histone methylation, peptidyl-lysine methylation, histone H3-K9 methylation; LOCATED IN: nucleus; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: SET domain (InterPro:IPR001214), SRA-YDG (InterPro:IPR003105), Pre-SET domain (InterPro:IPR007728), Post-SET domain (InterPro:IPR003616); BEST Arabidopsis thaliana protein match is: SU(VAR)3-9 homolog 6 (TAIR:AT2G22740.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (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_003076.8 Reference assembly

      Range
      4501362..4506250
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001343303.1 → NP_001332445.1  histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4-like protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8BH29

    2. NM_121399.3 → NP_196900.1  histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4-like protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_196900.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8GZB6, Q9C5P3, Q9FFX9
      UniProtKB/TrEMBL
      A0A5S9Y4H8, A0A654G0S6
      Conserved Domains (2) summary
      cd10545
      Location:360 → 595
      SET_AtSUVH-like; SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar proteins
      pfam02182
      Location:147 → 303
      SAD_SRA; SAD/SRA domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8GZB6.2

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