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clr4 histone H3 methyltransferase Clr4 [ Schizosaccharomyces pombe (fission yeast) ]

Gene ID: 2540825, updated on 11-Apr-2024

Summary

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Gene symbol
clr4
Gene description
histone H3 methyltransferase Clr4
Locus tag
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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Location:
chromosome: II
Exon count:
1
Sequence:
Chromosome: II; NC_003423.3 (453996..458487, complement)

Chromosome II - NC_003423.3Genomic Context describing neighboring genes Neighboring gene putative nuclear membrane organization protein Apq12 Neighboring gene miscRNA Neighboring gene putative argininosuccinate synthase Neighboring gene histone deacetylase complex subunit Rxt2 Neighboring gene meiotic chromosome segregation protein Meu6 Neighboring gene miscRNA Neighboring gene miscRNA Neighboring gene miscRNA Neighboring gene uncharacterized protein

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. SUV39 SET domains mediate crosstalk of heterochromatic histone marks. Stirpe A, et al. Elife, 2021 Sep 15. PMID 34524082, Free PMC Article
  2. 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
  3. 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
  4. Epigenetics. Epigenetic inheritance uncoupled from sequence-specific recruitment. Ragunathan K, et al. Science, 2015 Apr 3. PMID 25831549, Free PMC Article
  5. 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

See all (85) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. Sir2 is required for Clr4 to initiate centromeric heterochromatin assembly.
    Title: Sir2 is required for Clr4 to initiate centromeric heterochromatin assembly in fission yeast.
  9. 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.
  10. Data show that although Ers1 failed to bind Clr4, a direct interaction with Swi6 was detected, and centromeric localization of Swi6 was enhanced by Clr4 overexpression.
    Title: Heterochromatin protein 1 homologue Swi6 acts in concert with Ers1 to regulate RNAi-directed heterochromatin assembly.
Submit: New GeneRIF Correction See all GeneRIFs (21)

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-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 
Component Evidence Code Pubs
part_of CLRC complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of mating-type region heterochromatin NAS
Non-traceable Author Statement
more info
  
is_active_in nucleus HDA PubMed 
part_of pericentric heterochromatin TAS
Traceable Author Statement
more info
 PubMed 
part_of subtelomeric heterochromatin IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
histone H3 methyltransferase 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..458487 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001021094.2 → NP_595186.1  histone H3 methyltransferase 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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