HMGB2 high mobility group box 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HMGB2provided by HGNC
Official Full Name: high mobility group box 2provided by HGNC
Primary source: HGNC:HGNC:5000
See related: Ensembl:ENSG00000164104 MIM:163906
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: HMG2
Summary: This gene encodes a member of the non-histone chromosomal high mobility group protein family. The proteins of this family are chromatin-associated and ubiquitously distributed in the nucleus of higher eukaryotic cells. In vitro studies have demonstrated that this protein is able to efficiently bend DNA and form DNA circles. These studies suggest a role in facilitating cooperative interactions between cis-acting proteins by promoting DNA flexibility. This protein was also reported to be involved in the final ligation step in DNA end-joining processes of DNA double-strand breaks repair and V(D)J recombination. [provided by RefSeq, Jul 2008]
Expression: Biased expression in bone marrow (RPKM 603.0), lymph node (RPKM 141.8) and 10 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q34.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
109.20210226	current	GRCh38.p13 (GCF_000001405.39)	4	NC_000004.12 (173331376..173334358, complement)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (174252527..174255509, complement)

Chromosome 4 - NC_000004.12 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?

Bioinformatics analysis of the prognosis and biological significance of HMGB1, HMGB2, and HMGB3 in gastric cancer.
Title: Bioinformatics analysis of the prognosis and biological significance of HMGB1, HMGB2, and HMGB3 in gastric cancer.
Elevated hsa-miR-590-3p expression down-regulates HMGB2 expression and contributes to the severity of IgA nephropathy.
Title: Elevated hsa-miR-590-3p expression down-regulates HMGB2 expression and contributes to the severity of IgA nephropathy.
High-mobility group box 2 promoted proliferation of cervical cancer cells by activating AKT signaling pathway.
Title: High-mobility group box 2 promoted proliferation of cervical cancer cells by activating AKT signaling pathway.
lncRNA HOXA11-AS was overexpressed in glioma and overexpression was correlated with advanced stages of glioma and poor prognosis. Downregulating HOXA11-AS expression significantly suppressed proliferation, migration and invasion of glioma cells and increased their apoptosis. HOXA11-AS exerted its oncogenic effects by binding to miR-130a-5p, thereby neutralizing the suppressive effect of miR-130a-5p on HMGB2.
Title: The lncRNA HOXA11-AS promotes glioma cell growth and metastasis by targeting miR-130a-5p/HMGB2.
impact of HMGB1/2 KD on telomerase transcriptional regulation observed in neuroectodermal cells is partially masked in hESCs by their pluripotent state. Our findings on differential roles of HMGB1 and HMGB2 proteins in regulation of telomerase activity may suggest another possible outcome of HMGB1 targeting in cells, which is currently a promising approach aiming at increasing the anticancer activity of cytotoxic agents
Title: HMGB2 is a negative regulator of telomerase activity in human embryonic stem and progenitor cells.
Retention of DNA topoisomerase I (TOP1) to cytoplasmic chromatin depends on its stabilization by the chromatin architecture protein HMGB2. Functionally, the HMGB2-TOP1cc-cGAS axis determines the response of orthotopically transplanted ex vivo therapy-induced senescent cells to immune checkpoint blockade in vivo. HMGB2-TOP1cc-cGAS axis enables cytoplasmic chromatin recognition and response to immune checkpoint blockade.
Title: Topoisomerase 1 cleavage complex enables pattern recognition and inflammation during senescence.
HMGB2 is a novel prognostic biomarker for survival in gastric cancer
Title: HMGB2 promotes the malignancy of human gastric cancer and indicates poor survival outcome.
Knockdown of HMGB2 expression by stable transfected shRNA significantly decreased the growth and glycolysis of breast cancer cells both in vitro and in mouse models.
Title: HMGB2 is associated with malignancy and regulates Warburg effect by targeting LDHB and FBP1 in breast cancer.
HMBG2 overexpression promotes ischemia/reperfusion-induced cell apoptosis through activating the JNK1/2-NF-kappaBp65 signaling in AC16 cardiomyocytes.
Title: Involvement of JNK1/2-NF-κBp65 in the regulation of HMGB2 in myocardial ischemia/reperfusion-induced apoptosis in human AC16 cardiomyocytes.
Authors demonstrate that HMGB2 transcription is repressed by p21 during radiation-induced senescence through the ATM-p53-p21 DNA damage signaling cascade. The loss of p21 abolished the downregulation of HMGB2 caused by ionizing radiation, and the conditional induction of p21 was sufficient to repress the transcription of HMGB2.
Title: Transcriptional Repression of High-Mobility Group Box 2 by p21 in Radiation-Induced Senescence.

Submit: New GeneRIF Correction See all GeneRIFs (41)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-12669 (e-PCR)
- UniSTS:73475

PMC170950P6 (e-PCR)
- UniSTS:271624

HMGB2 (e-PCR)
- UniSTS:503325

SHGC-67901 (e-PCR)
- UniSTS:49708

HMGB2_3099 (e-PCR)
- UniSTS:462899

SHGC-60210 (e-PCR)
- UniSTS:68948

RH126943 (e-PCR)
- UniSTS:209768

RH101915 (e-PCR)
- UniSTS:96250

Homology

Homologs of the HMGB2 gene: The HMGB2 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, chicken, zebrafish, fruit fly, mosquito, and C.elegans.
Orthologs from Annotation Pipeline: 300 organisms have orthologs with human gene HMGB2
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
DNA binding, bending	IBA Inferred from Biological aspect of Ancestor more info	PubMed
DNA binding, bending	IDA Inferred from Direct Assay more info	PubMed
RAGE receptor binding	IGI Inferred from Genetic Interaction more info	PubMed
RNA binding	HDA more info	PubMed
chemoattractant activity	IDA Inferred from Direct Assay more info	PubMed
cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
damaged DNA binding	IDA Inferred from Direct Assay more info	PubMed
double-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
four-way junction DNA binding	ISS Inferred from Sequence or Structural Similarity more info
non-sequence-specific DNA binding, bending	ISS Inferred from Sequence or Structural Similarity more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein domain specific binding	IEA Inferred from Electronic Annotation more info
single-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
supercoiled DNA binding	ISS Inferred from Sequence or Structural Similarity more info
transcription coactivator activity	IDA Inferred from Direct Assay more info	PubMed
transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
DNA geometric change	ISS Inferred from Sequence or Structural Similarity more info
DNA topological change	ISS Inferred from Sequence or Structural Similarity more info
V(D)J recombination	ISS Inferred from Sequence or Structural Similarity more info
apoptotic DNA fragmentation	TAS Traceable Author Statement more info
cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
cellular response to lipopolysaccharide	IEP Inferred from Expression Pattern more info	PubMed
chromatin organization	NAS Non-traceable Author Statement more info	PubMed
defense response to Gram-negative bacterium	IDA Inferred from Direct Assay more info	PubMed
defense response to Gram-positive bacterium	IDA Inferred from Direct Assay more info	PubMed
double-strand break repair via nonhomologous end joining	ISS Inferred from Sequence or Structural Similarity more info
inflammatory response to antigenic stimulus	ISS Inferred from Sequence or Structural Similarity more info
innate immune response	IEA Inferred from Electronic Annotation more info
male gonad development	IEA Inferred from Electronic Annotation more info
negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	IEA Inferred from Electronic Annotation more info
negative regulation of transcription, DNA-templated	IDA Inferred from Direct Assay more info	PubMed
nucleosome assembly	NAS Non-traceable Author Statement more info	PubMed
positive chemotaxis	IEA Inferred from Electronic Annotation more info
positive regulation of DNA binding	IDA Inferred from Direct Assay more info	PubMed
positive regulation of endothelial cell proliferation	IDA Inferred from Direct Assay more info	PubMed
positive regulation of erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of innate immune response	IEA Inferred from Electronic Annotation more info
positive regulation of interferon-beta production	IEA Inferred from Electronic Annotation more info
positive regulation of megakaryocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of nuclease activity	IDA Inferred from Direct Assay more info	PubMed
positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
positive regulation of transcription, DNA-templated	IDA Inferred from Direct Assay more info	PubMed
regulation of neurogenesis	ISS Inferred from Sequence or Structural Similarity more info
regulation of stem cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
response to lipopolysaccharide	ISS Inferred from Sequence or Structural Similarity more info
response to steroid hormone	IEA Inferred from Electronic Annotation more info
spermatid nucleus differentiation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
chromatin	ISS Inferred from Sequence or Structural Similarity more info
condensed chromosome	IDA Inferred from Direct Assay more info	PubMed
cytoplasm	IDA Inferred from Direct Assay more info	PubMed
extracellular space	IDA Inferred from Direct Assay more info	PubMed
nucleolus	IDA Inferred from Direct Assay more info
nucleoplasm	IDA Inferred from Direct Assay more info
nucleoplasm	TAS Traceable Author Statement more info
nucleus	IDA Inferred from Direct Assay more info	PubMed
perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: high mobility group protein B2

Names: HMG-2; high mobility group protein 2; high-mobility group (nonhistone chromosomal) protein 2

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_001130688.1 → NP_001124160.1 high mobility group protein B2

See identical proteins and their annotated locations for NP_001124160.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1.

Source sequence(s)

AA576809, AK311864, BM727941

Consensus CDS

CCDS3816.1

UniProtKB/Swiss-Prot

P26583

Related

ENSP00000393448.2, ENST00000446922.6

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
NM_001130689.1 → NP_001124161.1 high mobility group protein B2

See identical proteins and their annotated locations for NP_001124161.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1.

Source sequence(s)

AA576809, AC097534, BM727941, BM781845

Consensus CDS

CCDS3816.1

UniProtKB/Swiss-Prot

P26583

Related

ENSP00000404912.2, ENST00000438704.6

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
NM_002129.4 → NP_002120.1 high mobility group protein B2

See identical proteins and their annotated locations for NP_002120.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript.

Source sequence(s)

AA576809, AC097534, BM727941

Consensus CDS

CCDS3816.1

UniProtKB/Swiss-Prot

P26583

Related

ENSP00000296503.5, ENST00000296503.10

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain