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    clr4 histone lysine H3-K9 methyltransferase (Suv39) Clr4 [ Schizosaccharomyces pombe (fission yeast) ]

    Gene ID: 2540825, updated on 18-Sep-2024

    Summary

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    Official Symbol
    clr4
    Official Full Name
    histone lysine H3-K9 methyltransferase (Suv39) Clr4
    Primary source
    PomBase:SPBC428.08c
    Locus tag
    SPOM_SPBC428.08C
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Schizosaccharomyces pombe (strain: 972h-)
    Lineage
    Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces
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    Genomic context

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    See clr4 in Genome Data Viewer
    Location:
    chromosome: II
    Exon count:
    1
    Sequence:
    Chromosome: II; NC_003423.3 (453996..458410, complement)

    Chromosome II - NC_003423.3Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene pleckstrin homology domain protein Meu6 Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene uncharacterized protein Neighboring gene ncRNA

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003423.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly. Khanduja JS, et al. Cell, 2024 Jun 20. PMID 38815580,
    2. SUV39 SET domains mediate crosstalk of heterochromatic histone marks. Stirpe A, et al. Elife, 2021 Sep 15. PMID 34524082, Free PMC Article
    3. Spreading and epigenetic inheritance of heterochromatin require a critical density of histone H3 lysine 9 tri-methylation. Cutter DiPiazza AR, et al. Proc Natl Acad Sci U S A, 2021 Jun 1. PMID 34035174, Free PMC Article
    4. The Clr4 methyltransferase determines the subnuclear localization of the mating-type region in fission yeast. Alfredsson-Timmins J, et al. J Cell Sci, 2007 Jun 1. PMID 17504808
    5. Mechanistic Insights into the Allosteric Regulation of the Clr4 Protein Lysine Methyltransferase by Autoinhibition and Automethylation. Khella MS, et al. Int J Mol Sci, 2020 Nov 22. PMID 33266419, Free PMC Article

    See all (95) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly.
      Title: RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly.
    2. Spreading and epigenetic inheritance of heterochromatin require a critical density of histone H3 lysine 9 tri-methylation.
      Title: Spreading and epigenetic inheritance of heterochromatin require a critical density of histone H3 lysine 9 tri-methylation.
    3. Mechanistic Insights into the Allosteric Regulation of the Clr4 Protein Lysine Methyltransferase by Autoinhibition and Automethylation.
      Title: Mechanistic Insights into the Allosteric Regulation of the Clr4 Protein Lysine Methyltransferase by Autoinhibition and Automethylation.
    4. N-Terminus Does Not Govern Protein Turnover of Schizosaccharomyces pombe CENP-A.
      Title: N-Terminus Does Not Govern Protein Turnover of Schizosaccharomyces pombe CENP-A.
    5. Clr4 chromodomain binds the H3K9me3 tail. Both the chromodomain and the disordered region connecting the chromodomain and the SET domain bind the nucleosome core. Interaction of the disordered region with the nucleosome core is independent of H3K9me and contributes to H3K9me in vitro and in vivo. Those interactions with the nucleosome core contribute to de novo H3K9me deposition and to heterochromatin establishment.
      Title: Disordered region of H3K9 methyltransferase Clr4 binds the nucleosome and contributes to its activity.
    6. revelation of an autoinhibited conformation in the conserved H3K9 methyltransferase Clr4 (also known as Suv39h) of the fission yeast Schizosaccharomyces pombe that has a critical role in preventing aberrant heterochromatin formation
      Title: Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability.
    7. Survival in quiescence requires the euchromatic deployment of Clr4 by Ago1-associated small RNAs.
      Title: Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs.
    8. These results demonstrate how a direct "read-write" mechanism involving Clr4 propagates histone modifications and allows histones to act as carriers of epigenetic information.
      Title: Epigenetics. Epigenetic inheritance uncoupled from sequence-specific recruitment.
    9. Sir2 is required for Clr4 to initiate centromeric heterochromatin assembly.
      Title: Sir2 is required for Clr4 to initiate centromeric heterochromatin assembly in fission yeast.
    10. Division of Labor between the Chromodomains of HP1/Swi6 and Suv39/Clr4 Is Required for Productive Heterochromatin Assembly.
      Title: Division of labor between the chromodomains of HP1 and Suv39 methylase enables coordination of heterochromatin spread.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Gene Ontology Provided by PomBase

    Function Evidence Code Pubs
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9 methyltransferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables histone H3K9 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9 methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K9 monomethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9me2 methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone reader activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables histone reader activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-lysine N-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables single-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin binding EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables ubiquitin-modified histone reader activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in co-transcriptional gene silencing by RNA interference machinery IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear polyadenylation-dependent antisense transcript catabolic process EXP
    Inferred from Experiment
    more info
    		 PubMed 
    involved_in pericentric heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in siRNA-independent facultative heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in siRNA-mediated pericentric heterochromatin formation EXP
    Inferred from Experiment
    more info
    		 PubMed 
    involved_in silent mating-type cassette heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in subtelomeric heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of CLRC complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in mating-type region heterochromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus HDA PubMed 
    is_active_in pericentric heterochromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in subtelomeric heterochromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone lysine H3-K9 methyltransferase (Suv39) Clr4

    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_003423.3 Reference assembly

      Range
      453996..458410 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001021094.3 → NP_595186.1  histone lysine H3-K9 methyltransferase (Suv39) Clr4 [Schizosaccharomyces pombe]

      See identical proteins and their annotated locations for NP_595186.1

      Status: PROVISIONAL

      UniProtKB/Swiss-Prot
      O60016, O74565
      Conserved Domains (5) summary
      smart00468
      Location:209 → 312
      PreSET; N-terminal to some SET domains
      smart00298
      Location:7 → 62
      CHROMO; Chromatin organization modifier domain
      smart00317
      Location:329 → 451
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:474 → 489
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:1 → 489
      SET; SET domain-containing protein (function unknown) [General function prediction only]
    Nucleotide Protein
    Heading Accession and Version

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    Research Materials