Suv39h2 suppressor of variegation 3-9 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Suv39h2provided by MGI
Official Full Name: suppressor of variegation 3-9 2provided by MGI
Primary source: MGI:MGI:1890396
See related: Ensembl:ENSMUSG00000026646 AllianceGenome:MGI:1890396
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: KMT1B; D2Ertd544e; 4930507K23Rik; D030054H19Rik
Summary: Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; chromatin binding activity; and histone-lysine N-methyltransferase activity. Involved in histone H3-K9 methylation; negative regulation of circadian rhythm; and negative regulation of transcription, DNA-templated. Acts upstream of or within histone H3-K9 methylation and male meiotic nuclear division. Located in heterochromatin and nucleus. Is expressed in several structures, including alimentary system; brain; early embryo; genitourinary system; and limb. Orthologous to human SUV39H2 (SUV39H2 histone lysine methyltransferase). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in CNS E11.5 (RPKM 5.6), placenta adult (RPKM 3.1) and 21 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 A1; 2 1.95 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (3456852..3476085, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (3455815..3474986, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A loss-of-function variant in SUV39H2 identified in autism-spectrum disorder causes altered H3K9 trimethylation and dysregulation of protocadherin beta-cluster genes in the developing brain.
Title: A loss-of-function variant in SUV39H2 identified in autism-spectrum disorder causes altered H3K9 trimethylation and dysregulation of protocadherin β-cluster genes in the developing brain.
Extreme disruption of heterochromatin is required for accelerated hematopoietic aging.
Title: Extreme disruption of heterochromatin is required for accelerated hematopoietic aging.
The authors show here that the mouse Suv39h2 enzyme differs from Suv39h1 by containing an N-terminal basic domain that facilitates retention at mitotic chromatin and provides an additional affinity for major satellite repeat RNA.
Title: Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation.
Data indicate that histone methyltransferase Suv39h2 expression is up-regulated in the liver in liver steatosis.
Title: Suv39h2 deficiency ameliorates diet-induced steatosis in mice.
Repeat-associated, Suv39h-dependent H3K9me3 displays a dynamic distribution that differs in the epigenome of pluripotent versus more committed cells.
Title: Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells.
ESET histone methyltransferase can form a large, multi-protein complex(es) with mSin3A/B co-repressors and HDAC1/2 that participates in multiple pathways of transcriptional repression.
Title: An ERG (ets-related gene)-associated histone methyltransferase interacts with histone deacetylases 1/2 and transcription co-repressors mSin3A/B.
Taken together, the results indicate epigenetic regulation of telomere length in mammals by Suv39h1 and Suv39h2.
Title: Epigenetic regulation of telomere length in mammalian cells by the Suv39h1 and Suv39h2 histone methyltransferases.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (6) 1 citation
Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

ksks283 (e-PCR)
- UniSTS:514323

AI661365 (e-PCR)
- UniSTS:165141

NoName (e-PCR)
- UniSTS:234318

AU022550 (e-PCR)
- UniSTS:178563

PMC102198P2 (e-PCR)
- UniSTS:186755

AU022550 (e-PCR)
- UniSTS:167332

AA536750 (e-PCR)
- UniSTS:158911

Suv39h2 (e-PCR), detects polymorphism
- UniSTS:527571

RH124451 (e-PCR)
- UniSTS:161273

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables S-adenosyl-L-methionine binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone H3 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 methyltransferase activity	IGI Inferred from Genetic Interaction more info	PubMed
enables histone H3K9 methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9me2 methyltransferase activity	IGI Inferred from Genetic Interaction more info	PubMed
enables histone methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin-like ligase-substrate adaptor activity	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell cycle	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to hypoxia	ISO Inferred from Sequence Orthology more info	PubMed
involved_in chromatin organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromatin remodeling	IGI Inferred from Genetic Interaction more info	PubMed
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epigenetic programming in the zygotic pronuclei	ISO Inferred from Sequence Orthology more info
involved_in male meiotic nuclear division	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within 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 gene expression, epigenetic	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within rhythmic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, centromeric region	IEA Inferred from Electronic Annotation more info
part_of heterochromatin	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase SUV39H2

Names: H3-K9-HMTase 2; Suv39h histone methyltransferase; histone H3-K9 methyltransferase 2; su(var)3-9 homolog 2; suppressor of variegation 3-9 homolog 2

NP_073561.2

EC 2.1.1.355

XP_036018338.1

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.

mRNA and Protein(s)

NM_022724.4 → NP_073561.2 histone-lysine N-methyltransferase SUV39H2

See identical proteins and their annotated locations for NP_073561.2

Status: VALIDATED

Description

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

Source sequence(s)

AK083457, AL732620, CX227854

Consensus CDS

CCDS15652.1

UniProtKB/Swiss-Prot

Q8BNK2, Q9CUK3, Q9EQQ0, Q9JLP7

UniProtKB/TrEMBL

A0A0R4J074

Related

ENSMUSP00000027956.3, ENSMUST00000027956.9

Conserved Domains (3) summary

smart00317
Location:317 → 446

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

pfam00385
Location:119 → 164

Chromo; Chromo (CHRromatin Organization MOdifier) domain

pfam05033
Location:221 → 309

Pre-SET; Pre-SET motif

RNA

NR_027509.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1. The resulting transcript is a candidate for nonsense-mediated mRNA decay (NMD) and therefore is not thought to encode a protein.

Source sequence(s)

AK083457, AL732620, BY752501, CX227854

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

3456852..3476085 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036162445.1 → XP_036018338.1 histone-lysine N-methyltransferase SUV39H2 isoform X1

Conserved Domains (1) summary

cd10532
Location:15 → 257

SET_SUV39H2; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins