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    SUV39H2 SUV39H2 histone lysine methyltransferase [ Homo sapiens (human) ]

    Gene ID: 79723, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SUV39H2provided by HGNC
    Official Full Name
    SUV39H2 histone lysine methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:17287
    See related
    Ensembl:ENSG00000152455 MIM:606503; AllianceGenome:HGNC:17287
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    KMT1B
    Summary
    Enables cation binding activity; histone H3K9 methyltransferase activity; and ubiquitin-like ligase-substrate adaptor activity. Involved in epigenetic programming in the zygotic pronuclei. Acts upstream of or within cellular response to hypoxia and negative regulation of transcription by RNA polymerase II. Located in chromatin. Is active in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in testis (RPKM 10.3), lymph node (RPKM 2.1) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SUV39H2 in Genome Data Viewer
    Location:
    10p13
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (14878866..14904315)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (14892831..14918279)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (14920865..14946314)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3085 Neighboring gene Myb/SANT DNA binding domain containing 7 Neighboring gene heat shock protein family A (Hsp70) member 14 Neighboring gene SUV39H2 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2164 Neighboring gene NANOG hESC enhancer GRCh37_chr10:14946352-14947052 Neighboring gene DNA cross-link repair 1C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3087 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:14994732-14995460 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:14995461-14996188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2166 Neighboring gene meiosis/spermiogenesis associated 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:15033655-15034186 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:15034187-15034717 Neighboring gene olfactory receptor family 7 subfamily E member 110 pseudogene Neighboring gene olfactory receptor family 7 subfamily E member 26 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Novel polymorphisms in the SUV39H2 histone methyltransferase and the risk of lung cancer. Yoon KA, et al. Carcinogenesis, 2006 Nov. PMID 16774942
    2. Automethylation of SUV39H2, an oncogenic histone lysine methyltransferase, regulates its binding affinity to substrate proteins. Piao L, et al. Oncotarget, 2016 Apr 19. PMID 26988914, Free PMC Article
    3. Activity and specificity of the human SUV39H2 protein lysine methyltransferase. Schuhmacher MK, et al. Biochim Biophys Acta, 2015 Jan. PMID 25459750
    4. Identification of SUV39H2 as a potential oncogene in lung adenocarcinoma. Zheng Y, et al. Clin Epigenetics, 2018 Oct 22. PMID 30348215, Free PMC Article
    5. Histone methyltransferase SUV39H2 serves oncogenic roles in osteosarcoma. Piao L, et al. Oncol Rep, 2019 Jan. PMID 30542727

    See all (53) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. N6-methyadenosine modified SUV39H2 regulates homologous recombination through epigenetic repression of DUSP6 in gastric cancer.
      Title: N6-methyadenosine modified SUV39H2 regulates homologous recombination through epigenetic repression of DUSP6 in gastric cancer.
    2. Epigenetic hallmarks of age-related macular degeneration are recapitulated in a photosensitive mouse model.
      Title: Epigenetic hallmarks of age-related macular degeneration are recapitulated in a photosensitive mouse model.
    3. SUV39H2 elevation contributes to the progression of nasopharyngeal carcinoma via regulation of NRIP1
      Title: Elevated SUV39H2 attributes to the progression of nasopharyngeal carcinoma via regulation of NRIP1.
    4. Results discovered that SUV39H2 is a potential oncogene in lung adenocarcinoma, whose expression was elevated in tumor tissues. SUV39H2 could potentiate the tumorigenesis and invasion of lung adenocarcinoma cells, probably by repressing OPTN and STOM.
      Title: Identification of SUV39H2 as a potential oncogene in lung adenocarcinoma.
    5. Study revealed that high SUV39H2 expression positively predicted poor prognosis of CRC patients. Moreover, SUV39H2 promoted CRC proliferation in a SLIT1-dependent manner.
      Title: SUV39H2 promotes colorectal cancer proliferation and metastasis via tri-methylation of the SLIT1 promoter.
    6. Knockdown of SUV39H2 expression by specific siRNAs in human osteosarcoma cell lines markedly suppressed cancer cell growth and caused an increase in the population of cells in G1 phase and induced apoptosis. Overexpression of SUV39H2 promoted cell proliferation, which indicated that SUV39H2 may possess oncogenic activity in human osteosarcoma.
      Title: Histone methyltransferase SUV39H2 serves oncogenic roles in osteosarcoma.
    7. Our finding unveils a novel autoregulatory mechanism of SUV39H2 through lysine automethylation
      Title: Automethylation of SUV39H2, an oncogenic histone lysine methyltransferase, regulates its binding affinity to substrate proteins.
    8. Our data show that the differential expression of SUV39H1 and SUV39H2 is associated with genomic instability and that the modulation of these HMTases can be an attractive approach to prevent CLL evolution
      Title: Aberrant levels of SUV39H1 and SUV39H2 methyltransferase are associated with genomic instability in chronic lymphocytic leukemia.
    9. SUV39H2 functioned cooperatively with MAGE-A11 to increase androgen-dependent AR transcriptional activity.
      Title: Androgen receptor regulation by histone methyltransferase Suppressor of variegation 3-9 homolog 2 and Melanoma antigen-A11.
    10. histone H3 lysine 9 methylation reduction, which may be due to the downregulation of methyltransferase SUV39H2 and the upregulation of demethylase KDM4C, was found in CD4(+) T lymphocytes of Latent autoimmune diabetes in adults patients
      Title: Reduced Histone H3 Lysine 9 Methylation Contributes to the Pathogenesis of Latent Autoimmune Diabetes in Adults via Regulation of SUV39H2 and KDM4C.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis identifies new susceptibility loci for migraine.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ23414

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables S-adenosyl-L-methionine binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3 methyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables histone H3K9 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K9 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables ubiquitin-like ligase-substrate adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cellular response to hypoxia IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chromatin organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in circadian rhythm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in epigenetic programming in the zygotic pronuclei IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of gene expression, epigenetic ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromosome, centromeric region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase SUV39H2
    Names
    H3-K9-HMTase 2
    histone H3-K9 methyltransferase 2
    histone methyltransferase SUV39H2
    lysine N-methyltransferase 1B
    su(var)3-9 homolog 2
    suppressor of variegation 3-9 homolog 2
    NP_001180353.1
    NP_001180354.1
    NP_001180355.1
    NP_001180356.1
    NP_078946.1
    XP_011517964.1
    XP_047281697.1
    XP_054222708.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001193424.2 → NP_001180353.1  histone-lysine N-methyltransferase SUV39H2 isoform 1

      See identical proteins and their annotated locations for NP_001180353.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript, and encodes the longest isoform (1).
      Source sequence(s)
      BC007754, DB040298
      Consensus CDS
      CCDS53494.1
      UniProtKB/Swiss-Prot
      D3DRT4, Q5JSS4, Q5JSS5, Q6I9Y3, Q8ND06, Q9H5I1
      Related
      ENSP00000346997.6, ENST00000354919.11
      Conserved Domains (2) summary
      cd18639
      Location:47 → 95
      CD_SUV39H1_like; chromodomain of histone methyltransferase SUV39H1, and similar proteins
      cd10532
      Location:167 → 409
      SET_SUV39H2; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins

    2. NM_001193425.2 → NP_001180354.1  histone-lysine N-methyltransferase SUV39H2 isoform 2

      See identical proteins and their annotated locations for NP_001180354.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon compared to variant 1. This results in translation initiation from an in-frame, downstream AUG, and a shorter isoform (2) compared to isoform 1. Variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AC069544, AL360083, BC007754, BU928392
      Consensus CDS
      CCDS7104.1
      UniProtKB/Swiss-Prot
      Q9H5I1
      Conserved Domains (2) summary
      cd10532
      Location:107 → 349
      SET_SUV39H2; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins
      cl28914
      Location:1 → 35
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

    3. NM_001193426.2 → NP_001180355.1  histone-lysine N-methyltransferase SUV39H2 isoform 3

      See identical proteins and their annotated locations for NP_001180355.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate donor splice site at an internal coding exon compared to variant 1, maintaining the reading frame, and resulting in a shorter isoform (3) missing an internal protein segment compared compared to isoform 1.
      Source sequence(s)
      BC007754, BC029360
      Consensus CDS
      CCDS53493.1
      UniProtKB/Swiss-Prot
      Q9H5I1
      Related
      ENSP00000367576.3, ENST00000378325.7
      Conserved Domains (2) summary
      smart00317
      Location:100 → 193
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      pfam00385
      Location:47 → 93
      Chromo; Chromo (CHRromatin Organisation MOdifier) domain

    4. NM_001193427.2 → NP_001180356.1  histone-lysine N-methyltransferase SUV39H2 isoform 4

      See identical proteins and their annotated locations for NP_001180356.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains an alternate 5' terminal exon, and uses an alternate donor splice site at an internal coding exon compared to variant 1. This results in translation initiation from an in-frame, downstream AUG, and a shorter isoform (4) missing an internal protein segment compared compared to isoform 1.
      Source sequence(s)
      BC007754, BU928392
      UniProtKB/TrEMBL
      Q5JSS2
      Related
      ENSP00000388968.1, ENST00000433779.5
      Conserved Domains (2) summary
      smart00317
      Location:40 → 133
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      pfam00385
      Location:2 → 33
      Chromo; Chromo (CHRromatin Organisation MOdifier) domain

    5. NM_024670.4 → NP_078946.1  histone-lysine N-methyltransferase SUV39H2 isoform 2

      See identical proteins and their annotated locations for NP_078946.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon, and is missing the subsequent exon compared to variant 1. This results in translation initiation from an in-frame, downstream AUG, and a shorter isoform (2) compared to isoform 1. Variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AC069544, BC007754
      Consensus CDS
      CCDS7104.1
      UniProtKB/Swiss-Prot
      Q9H5I1
      Related
      ENSP00000319208.5, ENST00000313519.9
      Conserved Domains (2) summary
      cd10532
      Location:107 → 349
      SET_SUV39H2; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins
      cl28914
      Location:1 → 35
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

    RNA

    1. NR_034181.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) is missing an internal exon compared to variant 1. It is represented as non-coding because the use of the 5'-most supported translational start codon as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK225369, BC007754, DB040298
      Related
      ENST00000378331.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      14878866..14904315
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425741.1 → XP_047281697.1  histone-lysine N-methyltransferase SUV39H2 isoform X1

    2. XM_011519662.3 → XP_011517964.1  histone-lysine N-methyltransferase SUV39H2 isoform X1

      See identical proteins and their annotated locations for XP_011517964.1

      UniProtKB/Swiss-Prot
      Q9H5I1
      Conserved Domains (2) summary
      cd10532
      Location:107 → 349
      SET_SUV39H2; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins
      cl28914
      Location:1 → 35
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      14892831..14918279
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366733.1 → XP_054222708.1  histone-lysine N-methyltransferase SUV39H2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H5I1.2 GenPept UniProtKB/Swiss-Prot:Q9H5I1

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