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

Gene ID: 79723, updated on 11-Apr-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 S-adenosyl-L-methionine binding activity; histone methyltransferase activity (H3-K9 specific); and zinc ion binding activity. Involved in chromatin assembly or disassembly and chromatin remodeling. Acts upstream of or within cellular response to hypoxia and negative regulation of transcription by RNA polymerase II. Located in chromatin. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
10p13
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (14878866..14904315)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (14892831..14918279)
105.20220307 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. Histone methyltransferase SUV39H2 serves oncogenic roles in osteosarcoma. Piao L, et al. Oncol Rep, 2019 Jan. PMID 30542727
  2. Identification of SUV39H2 as a potential oncogene in lung adenocarcinoma. Zheng Y, et al. Clin Epigenetics, 2018 Oct 22. PMID 30348215, Free PMC Article
  3. 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
  4. Activity and specificity of the human SUV39H2 protein lysine methyltransferase. Schuhmacher MK, et al. Biochim Biophys Acta, 2015 Jan. PMID 25459750
  5. Novel polymorphisms in the SUV39H2 histone methyltransferase and the risk of lung cancer. Yoon KA, et al. Carcinogenesis, 2006 Nov. PMID 16774942

See all (51) 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)

Genotypes

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 cycle IEA
Inferred from Electronic Annotation
more info
  
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
part_of 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_2023_10

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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