SUV39H1 SUV39H1 histone lysine methyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: SUV39H1provided by HGNC
Official Full Name: SUV39H1 histone lysine methyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:11479
See related: Ensembl:ENSG00000101945 MIM:300254; AllianceGenome:HGNC:11479
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MG44; KMT1A; SUV39H; H3-K9-HMTase 1
Summary: This gene encodes an evolutionarily-conserved protein containing an N-terminal chromodomain and a C-terminal SET domain. The encoded protein is a histone methyltransferase that trimethylates lysine 9 of histone H3, which results in transcriptional gene silencing. Loss of function of this gene disrupts heterochromatin formation and may cause chromosome instability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
Expression: Ubiquitous expression in bone marrow (RPKM 4.9), lymph node (RPKM 3.6) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xp11.23

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (48695554..48709016)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (48106035..48119497)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (48553945..48567407)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Histone methyltransferase Suv39h1 regulates hepatic stellate cell activation and is targetable in liver fibrosis.
Title: Histone methyltransferase Suv39h1 regulates hepatic stellate cell activation and is targetable in liver fibrosis.
The Wnt-pathway corepressor TLE3 interacts with the histone methyltransferase KMT1A to inhibit differentiation in Rhabdomyosarcoma.
Title: The Wnt-pathway corepressor TLE3 interacts with the histone methyltransferase KMT1A to inhibit differentiation in Rhabdomyosarcoma.
SUV39H1 is a novel biomarker targeting oxidative phosphorylation in hepatitis B virus-associated hepatocellular carcinoma.
Title: SUV39H1 is a novel biomarker targeting oxidative phosphorylation in hepatitis B virus-associated hepatocellular carcinoma.
SUV39H1 is a prognosis and immune microenvironment-related biomarker in diffuse large B-cell lymphoma.
Title: SUV39H1 is a prognosis and immune microenvironment-related biomarker in diffuse large B-cell lymphoma.
Decreased SUV39H1 at the promoter region leads to increased CREMalpha and accelerates autoimmune response in CD4[+] T cells from patients with systemic lupus erythematosus.
Title: Decreased SUV39H1 at the promoter region leads to increased CREMα and accelerates autoimmune response in CD4(+) T cells from patients with systemic lupus erythematosus.
Differences in SUV39H1 and androgen receptor distribution in adenomyomatous hyperplasia and prostatic adenocarcinoma.
Title: Differences in SUV39H1 and androgen receptor distribution in adenomyomatous hyperplasia and prostatic adenocarcinoma.
CD8+T cell responsiveness to anti-PD-1 is epigenetically regulated by Suv39h1 in melanomas.
Title: CD8+T cell responsiveness to anti-PD-1 is epigenetically regulated by Suv39h1 in melanomas.
Histone Mark Profiling in Pediatric Astrocytomas Reveals Prognostic Significance of H3K9 Trimethylation and Histone Methyltransferase SUV39H1.
Title: Histone Mark Profiling in Pediatric Astrocytomas Reveals Prognostic Significance of H3K9 Trimethylation and Histone Methyltransferase SUV39H1.
Suppressor of variegation 3-9 homologue 1 impairment and neutrophil-skewed systemic inflammation are associated with comorbidities in COPD.
Title: Suppressor of variegation 3-9 homologue 1 impairment and neutrophil-skewed systemic inflammation are associated with comorbidities in COPD.
EBP1 regulates Suv39H1 stability via the ubiquitin-proteasome system in neural development.
Title: EBP1 regulates Suv39H1 stability via the ubiquitin-proteasome system in neural development.

Submit: New GeneRIF Correction See all GeneRIFs (74)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	COUP-TF-interacting protein 2 (CTIP2) abolishes Vpr-mediated stimulation of p21 by cooperating with SUV39H1 and HDAC1/HDAC2 to silence the p21 gene transcription	PubMed

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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

DXS7466E (e-PCR)
- UniSTS:99329

DXS8281 (e-PCR)
- UniSTS:66119

PMC24455P1 (e-PCR)
- UniSTS:272257

DXS9868E (e-PCR)
- UniSTS:474282

WI-18178 (e-PCR)
- UniSTS:47852

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables S-adenosylmethionine-dependent methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	TAS Traceable Author Statement more info	PubMed
enables histone H3 methyltransferase activity	TAS Traceable Author Statement more info
enables histone H3K9 methyltransferase activity	EXP Inferred from Experiment more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables histone methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
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 zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in cell cycle	IEA Inferred from Electronic Annotation more info
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to glucose starvation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cellular response to hypoxia	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin organization	TAS Traceable Author Statement more info	PubMed
involved_in circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
involved_in energy homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rDNA heterochromatin formation	IDA Inferred from Direct Assay more info	PubMed
involved_in rDNA heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rDNA heterochromatin formation	TAS Traceable Author Statement more info
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by glucose	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin silencing complex	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome, centromeric region	IEA Inferred from Electronic Annotation more info
located_in condensed nuclear chromosome	TAS Traceable Author Statement more info	PubMed
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
part_of eNoSc complex	IPI Inferred from Physical Interaction more info	PubMed
part_of heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear lamina	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
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
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
part_of rDNA heterochromatin	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone-lysine N-methyltransferase SUV39H1

Names: Su(var)3-9 homolog 1; histone H3-K9 methyltransferase 1; histone-lysine N-methyltransferase, H3 lysine-9 specific 1; lysine N-methyltransferase 1A; position-effect variegation 3-9 homolog; suppressor of variegation 3-9 homolog 1

NP_001269095.1

EC 2.1.1.355

NP_003164.1

EC 2.1.1.355

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.

Genomic

NG_012530.2 RefSeqGene

Range

4995..17277

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001282166.2 → NP_001269095.1 histone-lysine N-methyltransferase SUV39H1 isoform 1

See identical proteins and their annotated locations for NP_001269095.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AF019968, AK299900, AW327567, BC006238

Consensus CDS

CCDS65252.1

UniProtKB/Swiss-Prot

O43463

Related

ENSP00000337976.6, ENST00000337852.10

Conserved Domains (2) summary

cd18639
Location:54 → 102

CD_SUV39H1_like; chromodomain of histone methyltransferase SUV39H1, and similar proteins

cd10525
Location:169 → 423

SET_SUV39H1; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 1 (SUV39H1) and similar proteins
NM_003173.4 → NP_003164.1 histone-lysine N-methyltransferase SUV39H1 isoform 2

See identical proteins and their annotated locations for NP_003164.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC231533, AF019968, AW327567, BC006238

Consensus CDS

CCDS14304.1

UniProtKB/Swiss-Prot

B2R6E8, B4DST0, O43463, Q53G60, Q6FHK6

Related

ENSP00000365877.4, ENST00000376687.4

Conserved Domains (2) summary

cd18639
Location:43 → 91

CD_SUV39H1_like; chromodomain of histone methyltransferase SUV39H1, and similar proteins

cd10525
Location:158 → 412

SET_SUV39H1; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 1 (SUV39H1) and similar proteins