Gene description for Hmgb1
Gene name high mobility group box 1
Gene symbol Hmgb1
Other names/aliases DEF
HMG-1
Hmg1
SBP-1
amphoterin
p30
Species Mus musculus
 Database cross references - Hmgb1
ExoCarta ExoCarta_15289
Vesiclepedia VP_15289
Entrez Gene 15289
UniProt P63158  
 Hmgb1 identified in sEVs derived from the following tissue/cell type
Colon cancer cells 37309723    
Mast cells 17486113    
Pancreatic cells 19351151    
T-cell lymphoma cells 37309723    
 Gene ontology annotations for Hmgb1
Molecular Function
    four-way junction DNA binding GO:0000400 ISO
    four-way junction DNA binding GO:0000400 ISS
    open form four-way junction DNA binding GO:0000401 ISO
    crossed form four-way junction DNA binding GO:0000402 ISO
    bubble DNA binding GO:0000405 ISS
    transcription cis-regulatory region binding GO:0000976 ISO
    lipopolysaccharide binding GO:0001530 ISO
    phosphatidylserine binding GO:0001786 ISO
    phosphatidylserine binding GO:0001786 TAS
    nucleic acid binding GO:0003676 EXP
    bent DNA binding GO:0003681 ISO
    damaged DNA binding GO:0003684 ISO
    double-stranded DNA binding GO:0003690 IDA
    double-stranded DNA binding GO:0003690 ISO
    single-stranded DNA binding GO:0003697 ISO
    transcription coactivator activity GO:0003713 ISO
    transcription corepressor activity GO:0003714 ISO
    double-stranded RNA binding GO:0003725 IDA
    single-stranded RNA binding GO:0003727 IDA
    cytokine activity GO:0005125 IDA
    cytokine activity GO:0005125 ISO
    integrin binding GO:0005178 ISO
    protein binding GO:0005515 IPI
    5S rRNA binding GO:0008097 ISO
    heparin binding GO:0008201 IEA
    heparin binding GO:0008201 ISO
    DNA binding, bending GO:0008301 IBA
    DNA binding, bending GO:0008301 ISO
    DNA binding, bending GO:0008301 ISS
    calcium-dependent protein kinase regulator activity GO:0010858 IDA
    lyase activity GO:0016829 ISO
    C-X-C chemokine binding GO:0019958 ISO
    protein kinase activator activity GO:0030295 IDA
    peptide binding GO:0042277 ISO
    receptor ligand activity GO:0048018 ISO
    RAGE receptor binding GO:0050786 ISO
    glycolipid binding GO:0051861 ISO
    RNA polymerase II-specific DNA-binding transcription factor binding GO:0061629 ISO
    DNA polymerase binding GO:0070182 ISO
    supercoiled DNA binding GO:0097100 ISS
    DNA-binding transcription factor binding GO:0140297 ISO
Biological Process
    negative regulation of transcription by RNA polymerase II GO:0000122 ISO
    eye development GO:0001654 IMP
    myeloid dendritic cell activation GO:0001773 IMP
    positive regulation of protein phosphorylation GO:0001934 IDA
    endothelial cell proliferation GO:0001935 IDA
    positive regulation of mesenchymal cell proliferation GO:0002053 ISO
    activation of innate immune response GO:0002218 ISO
    adaptive immune response GO:0002250 IEA
    plasmacytoid dendritic cell activation GO:0002270 IMP
    macrophage activation involved in immune response GO:0002281 IMP
    myeloid progenitor cell differentiation GO:0002318 IDA
    regulation of tolerance induction GO:0002643 IMP
    regulation of tolerance induction GO:0002643 ISO
    regulation of T cell mediated immune response to tumor cell GO:0002840 IDA
    glycogen catabolic process GO:0005980 IMP
    base-excision repair GO:0006284 IMP
    DNA recombination GO:0006310 IEA
    chromatin organization GO:0006325 IDA
    regulation of transcription by RNA polymerase II GO:0006357 IBA
    transcription by RNA polymerase II GO:0006366 IMP
    autophagy GO:0006914 IEA
    inflammatory response GO:0006954 ISO
    inflammatory response GO:0006954 TAS
    signal transduction GO:0007165 IEA
    positive regulation of cytosolic calcium ion concentration GO:0007204 ISO
    positive regulation of autophagy GO:0010508 IMP
    positive regulation of autophagy GO:0010508 ISO
    negative regulation of RNA polymerase II transcription preinitiation complex assembly GO:0017055 ISO
    myeloid cell differentiation GO:0030099 IDA
    lung development GO:0030324 IMP
    positive regulation of cell migration GO:0030335 ISO
    regulation of restriction endodeoxyribonuclease activity GO:0032072 ISO
    DNA geometric change GO:0032392 ISO
    DNA geometric change GO:0032392 ISS
    positive regulation of mismatch repair GO:0032425 ISO
    negative regulation of type II interferon production GO:0032689 ISO
    positive regulation of interferon-alpha production GO:0032727 IMP
    positive regulation of interferon-beta production GO:0032728 IMP
    positive regulation of interleukin-1 beta production GO:0032731 IMP
    positive regulation of interleukin-1 production GO:0032732 ISO
    positive regulation of interleukin-10 production GO:0032733 ISO
    positive regulation of interleukin-12 production GO:0032735 ISO
    positive regulation of interleukin-6 production GO:0032755 IMP
    positive regulation of interleukin-6 production GO:0032755 ISO
    positive regulation of interleukin-8 production GO:0032757 ISO
    positive regulation of tumor necrosis factor production GO:0032760 IMP
    positive regulation of tumor necrosis factor production GO:0032760 ISO
    V(D)J recombination GO:0033151 ISO
    positive regulation of toll-like receptor 2 signaling pathway GO:0034137 IDA
    positive regulation of toll-like receptor 4 signaling pathway GO:0034145 IDA
    positive regulation of toll-like receptor 9 signaling pathway GO:0034165 ISS
    T-helper 1 cell activation GO:0035711 ISO
    endothelial cell chemotaxis GO:0035767 IDA
    positive regulation of activated T cell proliferation GO:0042104 ISO
    positive regulation of apoptotic process GO:0043065 ISO
    apoptotic cell clearance GO:0043277 ISO
    apoptotic cell clearance GO:0043277 ISS
    negative regulation of CD4-positive, alpha-beta T cell differentiation GO:0043371 ISO
    positive regulation of DNA binding GO:0043388 ISO
    positive regulation of MAPK cascade GO:0043410 ISO
    positive regulation of blood vessel endothelial cell migration GO:0043536 ISO
    negative regulation of blood vessel endothelial cell migration GO:0043537 ISO
    T-helper 1 cell differentiation GO:0045063 ISO
    innate immune response GO:0045087 IEA
    positive regulation of innate immune response GO:0045089 IMP
    positive regulation of myeloid cell differentiation GO:0045639 IDA
    positive regulation of glycogen catabolic process GO:0045819 IMP
    positive regulation of mitotic cell cycle GO:0045931 ISO
    positive regulation of transcription by RNA polymerase II GO:0045944 IMP
    positive regulation of transcription by RNA polymerase II GO:0045944 ISO
    positive regulation of JNK cascade GO:0046330 ISO
    positive regulation of viral entry into host cell GO:0046598 ISO
    induction of positive chemotaxis GO:0050930 ISO
    positive regulation of DNA ligation GO:0051106 ISS
    response to glucocorticoid GO:0051384 IMP
    positive regulation of ERK1 and ERK2 cascade GO:0070374 IDA
    positive regulation of ERK1 and ERK2 cascade GO:0070374 ISO
    cellular response to lipopolysaccharide GO:0071222 IDA
    positive regulation of monocyte chemotactic protein-1 production GO:0071639 IMP
    positive regulation of monocyte chemotaxis GO:0090026 ISO
    positive regulation of wound healing GO:0090303 IDA
    neutrophil clearance GO:0097350 ISO
    neutrophil clearance GO:0097350 ISS
    cellular response to interleukin-7 GO:0098761 IDA
    positive regulation of non-canonical NF-kappaB signal transduction GO:1901224 IDA
    positive regulation of sprouting angiogenesis GO:1903672 IDA
    positive regulation of myeloid progenitor cell differentiation GO:1905455 IDA
    positive regulation of vascular endothelial cell proliferation GO:1905564 ISO
    positive regulation of chemokine (C-X-C motif) ligand 2 production GO:2000343 ISO
    negative regulation of apoptotic cell clearance GO:2000426 ISO
    regulation of nucleotide-excision repair GO:2000819 IMP
    positive regulation of cysteine-type endopeptidase activity GO:2001056 ISO
    positive regulation of dendritic cell differentiation GO:2001200 ISO
Subcellular Localization
    condensed chromosome GO:0000793 ISO
    extracellular region GO:0005576 TAS
    extracellular space GO:0005615 IDA
    extracellular space GO:0005615 ISO
    extracellular space GO:0005615 ISO
    nucleus GO:0005634 IDA
    nucleus GO:0005634 ISO
    chromosome GO:0005694 IEA
    cytoplasm GO:0005737 IDA
    early endosome GO:0005769 IDA
    endoplasmic reticulum GO:0005783 ISO
    endoplasmic reticulum-Golgi intermediate compartment GO:0005793 IEA
    cytosol GO:0005829 ISO
    plasma membrane GO:0005886 IEA
    cell surface GO:0009986 ISO
    transcription repressor complex GO:0017053 ISO
    alphav-beta3 integrin-HMGB1 complex GO:0035868 ISO
    neuron projection GO:0043005 IDA
    membrane raft GO:0045121 ISO
 Experiment description of studies that identified Hmgb1 in sEVs
1
Experiment ID 907
MISEV standards
✔
EM
Biophysical techniques
✔
Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a
Enriched markers
✔
HSPA5
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 37309723    
Organism Mus musculus
Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells
Authors "Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."
Journal name Proteomics
Publication year 2023
Sample Colon cancer cells
Sample name C26
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
2
Experiment ID 15
MISEV standards
✔
EM
Biophysical techniques
✔
CD63
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule mrna
Identification method Microarray
PubMed ID 17486113    
Organism Mus musculus
Homo sapiens
Experiment description Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells.
Authors "Valadi H, Ekstrom K, Bossios A, Sjostrand M, Lee JJ, Lotvall JO"
Journal name NCB
Publication year 2007
Sample Mast cells
Sample name MC9
Bone marrow-derived mast cells
HMC-1
Isolation/purification methods Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.11-1.21 g/mL
Molecules identified in the study Protein
mRNA
miRNA
Methods used in the study Mass spectrometry [MALDI TOF]
Western blotting
Microarray
miRCURY LNA Array
3
Experiment ID 188
MISEV standards
✔
EM
Biophysical techniques
✔
GAPDH|UCHL1|HSP90
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 19351151    
Organism Mus musculus
Experiment description Characterization of vesicles secreted from insulinoma NIT-1 cells.
Authors "Lee HS, Jeong J, Lee KJ."
Journal name J Proteome Res
Publication year 2009
Sample Pancreatic cells
Sample name Pancreatic beta cell (NIT-1)
Isolation/purification methods Differential centrifugation
Sucrose density gradient
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
4
Experiment ID 908
MISEV standards
✔
EM
Biophysical techniques
✔
Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a
Enriched markers
✔
HSPA5
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 37309723    
Organism Mus musculus
Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells
Authors "Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."
Journal name Proteomics
Publication year 2023
Sample T-cell lymphoma cells
Sample name EL4
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
 Protein-protein interactions for Hmgb1
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 Mettl21e  
Affinity Capture-MS Mus musculus
2 Tmem173  
Proximity Label-MS Mus musculus
3 Atxn1  
Affinity Capture-MS Mus musculus
4 Kctd13  
Affinity Capture-MS Mus musculus
5 Tfe3  
Affinity Capture-MS Mus musculus
6 Tia1  
Affinity Capture-MS Mus musculus
View the network image/svg+xml
 Pathways in which Hmgb1 is involved
PathwayEvidenceSource
Advanced glycosylation endproduct receptor signaling IEA Reactome
Apoptosis IEA Reactome
Apoptosis induced DNA fragmentation IEA Reactome
Apoptotic execution phase IEA Reactome
Cytokine Signaling in Immune system IEA Reactome
DDX58/IFIH1-mediated induction of interferon-alpha/beta IEA Reactome
Immune System IEA Reactome
Innate Immune System IEA Reactome
Interleukin-1 family signaling IEA Reactome
Interleukin-1 signaling IEA Reactome
MyD88 cascade initiated on plasma membrane IEA Reactome
MyD88 dependent cascade initiated on endosome IEA Reactome
MyD88-independent TLR4 cascade IEA Reactome
MyD88:MAL(TIRAP) cascade initiated on plasma membrane IEA Reactome
Neutrophil degranulation IEA Reactome
Programmed Cell Death IEA Reactome
Pyroptosis IEA Reactome
Regulated Necrosis IEA Reactome
Regulation of TLR by endogenous ligand IEA Reactome
Signaling by Interleukins IEA Reactome
TAK1-dependent IKK and NF-kappa-B activation IEA Reactome
Toll Like Receptor 10 (TLR10) Cascade IEA Reactome
Toll Like Receptor 2 (TLR2) Cascade IEA Reactome
Toll Like Receptor 3 (TLR3) Cascade IEA Reactome
Toll Like Receptor 4 (TLR4) Cascade IEA Reactome
Toll Like Receptor 5 (TLR5) Cascade IEA Reactome
Toll Like Receptor 7/8 (TLR7/8) Cascade IEA Reactome
Toll Like Receptor 9 (TLR9) Cascade IEA Reactome
Toll Like Receptor TLR1:TLR2 Cascade IEA Reactome
Toll Like Receptor TLR6:TLR2 Cascade IEA Reactome
Toll-like Receptor Cascades IEA Reactome
TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation IEA Reactome
TRAF6 mediated NF-kB activation IEA Reactome
TRIF (TICAM1)-mediated TLR4 signaling IEA Reactome





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