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

Genomic context

Location:: 4q34.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
109.20190905	current	GRCh38.p13 (GCF_000001405.39)	4	NC_000004.12 (173331376..173334358, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (174252527..174255595, 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?

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.
Multiple functions of HMGB proteins reveal the complex roles of these proteins as innate and endogenous regulators of inflammation in joints and their cooperative roles in cartilage hypertrophy as well as in the maintenance of joint tissue homeostasis.
Title: HMGB proteins and arthritis.
identified the oncogene HMGB2 as a downstream target of miR-130a by using luciferase and western blot assays. Knockdown of HMGB2 mimicked the effect of miR-130a in glioma cells.
Title: Downregulation of miR-130a promotes cell growth and epithelial to mesenchymal transition by activating HMGB2 in glioma.
downregulation of HMGB1 and/or HMGB2 in undifferentiated human embryonic stem cells does not affect the stemness of cells.
Title: Properties of Human Embryonic Stem Cells and Their Differentiated Derivatives Depend on Nonhistone DNA-Binding HMGB1 and HMGB2 Proteins.
Serum HMGB2 levels were associated with in-stent restenosis in patients.
Title: Association of Serum HMGB2 Levels With In-Stent Restenosis: HMGB2 Promotes Neointimal Hyperplasia in Mice With Femoral Artery Injury and Proliferation and Migration of VSMCs.
results establish HMGB2 as a novel master regulator that orchestrates senescence-associated secretory phenotype.
Title: HMGB2 orchestrates the chromatin landscape of senescence-associated secretory phenotype gene loci.
Data indicate the function of high mobility group box 2 (HMGB2) in glycolytic control in pancreatic cancer.
Title: Expression of HMGB2 indicates worse survival of patients and is required for the maintenance of Warburg effect in pancreatic cancer.
data demonstrate a reciprocal relationship between Hmgb2 and Ctcf in controlling aspects of chromatin structure and gene expression.
Title: Reciprocal Regulation of the Cardiac Epigenome by Chromatin Structural Proteins Hmgb and Ctcf: IMPLICATIONS FOR TRANSCRIPTIONAL REGULATION.

Submit: New GeneRIF Correction See all GeneRIFs (34)

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)

Pathways from BioSystems

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Activation of DNA fragmentation factor, organism-specific biosystem (from REACTOME)
Activation of DNA fragmentation factor, organism-specific biosystemDNA fragmentation in response to apoptotic signals is achieved, in part, through the activity of apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) (reviewed ...
Apoptosis, organism-specific biosystem (from REACTOME)
Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
Apoptosis induced DNA fragmentation, organism-specific biosystem (from REACTOME)
Apoptosis induced DNA fragmentation, organism-specific biosystemDNA fragmentation in response to apoptotic signals is achieved through the activity of two apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease...
Apoptotic execution phase, organism-specific biosystem (from REACTOME)
Apoptotic execution phase, organism-specific biosystemIn the execution phase of apoptosis, effector caspases cleave vital cellular proteins leading to the morphological changes that characterize apoptosis. These changes include destruction of the nucle...
Ectoderm Differentiation, organism-specific biosystem (from WikiPathways)
Ectoderm Differentiation, organism-specific biosystemModel depicting ectoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
Programmed Cell Death, organism-specific biosystem (from REACTOME)
Programmed Cell Death, organism-specific biosystemCell death is a fundamental cellular response that has a crucial role in shaping our bodies during development and in regulating tissue homeostasis by eliminating unwanted cells. There are a number o...
Retinoblastoma (RB) in Cancer, organism-specific biosystem (from WikiPathways)
Retinoblastoma (RB) in Cancer, organism-specific biosystemDescribes the role of retinoblastoma (RB) gene in cancer.

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: 237 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
damaged DNA binding	IDA Inferred from Direct Assay more info	PubMed
double-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
drug binding	ISS Inferred from Sequence or Structural Similarity more info
enhancer sequence-specific 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	IBA Inferred from Biological aspect of Ancestor more info	PubMed
transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
transcription regulatory region 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 ligation involved in DNA repair	ISS Inferred from Sequence or Structural Similarity more info
DNA recombination	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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
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	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	IBA Inferred from Biological aspect of Ancestor 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 drug	ISS Inferred from Sequence or Structural Similarity more info
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
cell	IDA Inferred from Direct Assay more info	PubMed
condensed chromosome	IDA Inferred from Direct Assay more info	PubMed
cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
cytoplasm	IDA Inferred from Direct Assay more info	PubMed
extracellular space	IDA Inferred from Direct Assay more info	PubMed
nuclear chromatin	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nuclear chromatin	ISS Inferred from Sequence or Structural Similarity more info
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

cl00082
Location:10 → 78

HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
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

cl00082
Location:10 → 78

HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
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

cl00082
Location:10 → 78

HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...