Gene description for HIST1H3B
Gene name histone cluster 1, H3b
Gene symbol HIST1H3B
Other names/aliases H3/l
H3FL
Species Homo sapiens
 Database cross references - HIST1H3B
ExoCarta ExoCarta_8358
Vesiclepedia VP_8358
Entrez Gene 8358
HGNC 4776
MIM 602819
UniProt P68431  
 HIST1H3B identified in exosomes derived from the following tissue/cell type
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Endothelial cells 26027894    
Neuroblastoma cells 25944692    
Prostate cancer cells 22723089    
Prostate cancer cells 22723089    
Prostate cancer cells 22723089    
Prostate cancer cells 22723089    
Squamous carcinoma cells 20124223    
Thymus 23844026    
 Gene ontology annotations for HIST1H3B
Molecular Function
    DNA binding GO:0003677 IEA
    protein binding GO:0005515 IDA
    protein binding GO:0005515 IPI
    structural constituent of chromatin GO:0030527 IEA
    cadherin binding GO:0045296 HDA
    protein heterodimerization activity GO:0046982 IEA
Biological Process
    chromatin organization GO:0006325 NAS
    nucleosome assembly GO:0006334 IDA
    nucleosome assembly GO:0006334 IMP
    gene expression GO:0010467 IDA
    telomere organization GO:0032200 TAS
    epigenetic regulation of gene expression GO:0040029 IDA
Subcellular Localization
    nucleosome GO:0000786 IDA
    nucleosome GO:0000786 IPI
    extracellular region GO:0005576 TAS
    nucleus GO:0005634 HDA
    nucleus GO:0005634 IDA
    nucleoplasm GO:0005654 IDA
    nucleoplasm GO:0005654 TAS
    membrane GO:0016020 HDA
    protein-containing complex GO:0032991 IDA
    extracellular exosome GO:0070062 HDA
 Experiment description of studies that identified HIST1H3B in exosomes
1
Experiment ID 282
MISEV standards
✔
CEM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81|EpCAM
Enriched markers
✘ Negative markers
✔
DLS
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors "Xu R, Greening DW, Rai A, Ji H, Simpson RJ."
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Ultracentrifugation - Rep 1
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
2
Experiment ID 283
MISEV standards
✔
CEM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81|EpCAM
Enriched markers
✘ Negative markers
✔
DLS
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors "Xu R, Greening DW, Rai A, Ji H, Simpson RJ."
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Ultracentrifugation - Rep 2
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
3
Experiment ID 285
MISEV standards
✔
CEM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81|EpCAM
Enriched markers
✘ Negative markers
✔
DLS
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors "Xu R, Greening DW, Rai A, Ji H, Simpson RJ."
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Sequential centrifugal ultrafiltration - Rep 1
Isolation/purification methods Differential centrifugation
Filtration
Sequential centrifugal ultrafiltration
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
4
Experiment ID 286
MISEV standards
✔
CEM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81|EpCAM
Enriched markers
✘ Negative markers
✔
DLS
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors "Xu R, Greening DW, Rai A, Ji H, Simpson RJ."
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Sequential centrifugal ultrafiltration - Rep 2
Isolation/purification methods Differential centrifugation
Filtration
Sequential centrifugal ultrafiltration
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
5
Experiment ID 226
MISEV standards
✔
EM
Biophysical techniques
✔
GAPDH|CD9|FLOT1
Enriched markers
✔
LMNA|H2AFX|ATP5A1|TOMM20
Negative markers
✘ Particle analysis
Identified molecule mRNA
Identification method Small RNA sequencing (Illumina HiSeq 2000 (Solexa)
PubMed ID 26027894    
Organism Homo sapiens
Experiment description "Quantitative and qualitative analysis of small RNAs in human endothelial cells and exosomes provides insights into localized RNA processing, degradation and sorting"
Authors "Bas W. M. van Balkom, Almut S. Eisele, D. Michiel Pegtel, Sander Bervoets, Marianne C. Verhaar"
Journal name Journal of Extracellular Vesicles
Publication year 2015
Sample Endothelial cells
Sample name HMEC-1
Isolation/purification methods Differential ultracentrifugation
Sucrose density gradient
Flotation density 1.10 g/mL
Molecules identified in the study miRNA
Protein
snoRNA
lncRNA
yRNA
snRNA
mRNA
ncRNA
mtRNA
vtRNA
scaRNA
lincRNA
Methods used in the study Small RNA sequencing (Illumina HiSeq 2000 (Solexa)
Western blotting
6
Experiment ID 224
MISEV standards
✔
EM|AFM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81
Enriched markers
✔
GOLGA2
Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25944692    
Organism Homo sapiens
Experiment description Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes
Authors "Keerthikumar S, Gangoda L, Liem M, Fonseka P, Atukorala I, Ozcitti C, Mechler A, Adda CG, Ang CS, Mathivanan S"
Journal name Oncotarget
Publication year 2015
Sample Neuroblastoma cells
Sample name SH-SY5Y
Isolation/purification methods Differential centrifugation
Ultracentrifugation
OptiPrep density gradient
Flotation density 1.10 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
7
Experiment ID 138
MISEV standards
✔
EM
Biophysical techniques
✔
HSP70|HSP90|RAB5|LAMP2|CD9
Enriched markers
✔
HSP90B1
Negative markers
✘ Particle analysis
Identified molecule protein
Identification method
Mass spectrometry [QTOF]   
PubMed ID 22723089    
Organism Homo sapiens
Experiment description Prostate cancer cell derived exosomes
Authors "Hosseini-Beheshti E, Guns ES."
Journal name MCP
Publication year 2012
Sample Prostate cancer cells
Sample name DU145 - Rep 2
Isolation/purification methods Sucrose density gradient
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry [QTOF]
8
Experiment ID 141
MISEV standards
✔
EM
Biophysical techniques
✔
HSP70|HSP90|RAB5|LAMP2|CD9
Enriched markers
✔
HSP90B1
Negative markers
✘ Particle analysis
Identified molecule protein
Identification method
Mass spectrometry [QTOF]   
PubMed ID 22723089    
Organism Homo sapiens
Experiment description Prostate cancer cell derived exosomes
Authors "Hosseini-Beheshti E, Guns ES."
Journal name MCP
Publication year 2012
Sample Prostate cancer cells
Sample name VCaP - Rep 3
Isolation/purification methods Sucrose density gradient
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry [QTOF]
9
Experiment ID 143
MISEV standards
✔
EM
Biophysical techniques
✔
HSP70|HSP90|RAB5|LAMP2|CD9
Enriched markers
✔
HSP90B1
Negative markers
✘ Particle analysis
Identified molecule protein
Identification method
Mass spectrometry [QTOF]   
PubMed ID 22723089    
Organism Homo sapiens
Experiment description Prostate cancer cell derived exosomes
Authors "Hosseini-Beheshti E, Guns ES."
Journal name MCP
Publication year 2012
Sample Prostate cancer cells
Sample name LNCaP - Rep 3
Isolation/purification methods Sucrose density gradient
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry [QTOF]
10
Experiment ID 144
MISEV standards
✔
EM
Biophysical techniques
✔
HSP70|HSP90|RAB5|CD9
Enriched markers
✔
HSP90B1
Negative markers
✘ Particle analysis
Identified molecule protein
Identification method
Mass spectrometry [QTOF]   
PubMed ID 22723089    
Organism Homo sapiens
Experiment description Prostate cancer cell derived exosomes
Authors "Hosseini-Beheshti E, Guns ES."
Journal name MCP
Publication year 2012
Sample Prostate cancer cells
Sample name C4-2 - Rep 2
Isolation/purification methods Sucrose density gradient
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry [QTOF]
11
Experiment ID 191
MISEV standards
✘ Biophysical techniques
✔
Alix|CD81|CD9
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 20124223    
Organism Homo sapiens
Experiment description Hypoxic tumor cell modulates its microenvironment to enhance angiogenic and metastatic potential by secretion of proteins and exosomes.
Authors "Park JE, Tan HS, Datta A, Lai RC, Zhang H, Meng W, Lim SK, Sze SK."
Journal name Mol Cell Proteomics
Publication year 2010
Sample Squamous carcinoma cells
Sample name Squamous carcinoma cell (A431)
Isolation/purification methods Differential centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
12
Experiment ID 217
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|CD81|CD9|CD63
Enriched markers
✘ Negative markers
✔
NTA
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23844026    
Organism Homo sapiens
Experiment description Characterization of human thymic exosomes.
Authors "Skogberg G, Gudmundsdottir J, van der Post S, Sandstrom K, Bruhn S, Benson M, Mincheva-Nilsson L, Baranov V, Telemo E, Ekwall O."
Journal name PLoS One
Publication year 2013
Sample Thymus
Sample name Normal-Thymus
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
 Protein-protein interactions for HIST1H3B
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 ZNF644  
Affinity Capture-MS Homo sapiens
2 IPO4 79711
Affinity Capture-MS Homo sapiens
3 WIZ 58525
Affinity Capture-MS Homo sapiens
4 PHF1  
Reconstituted Complex Homo sapiens
5 HIST2H3PS2 440686
Affinity Capture-MS Homo sapiens
6 CRTC2 200186
Affinity Capture-Western Homo sapiens
7 CBX1 10951
Affinity Capture-MS Homo sapiens
8 ASF1A 25842
Affinity Capture-MS Homo sapiens
9 MCM2 4171
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
10 LIG3 3980
Affinity Capture-MS Homo sapiens
11 HDGF 3068
Affinity Capture-MS Homo sapiens
12 NASP 4678
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
13 ASF1B  
Affinity Capture-MS Homo sapiens
14 XPC  
Affinity Capture-MS Homo sapiens
15 SSRP1 6749
Affinity Capture-MS Homo sapiens
16 H2AFZ 3015
Affinity Capture-MS Homo sapiens
17 RLIM 51132
Affinity Capture-MS Homo sapiens
18 RBBP7 5931
Affinity Capture-MS Homo sapiens
19 PDHA1 5160
Affinity Capture-MS Homo sapiens
20 HIST2H2AB 317772
Affinity Capture-MS Homo sapiens
21 UBR7  
Affinity Capture-MS Homo sapiens
22 TIMELESS  
Affinity Capture-MS Homo sapiens
23 TONSL  
Affinity Capture-MS Homo sapiens
24 HIST3H2BB 128312
Affinity Capture-MS Homo sapiens
25 MCM4 4173
Affinity Capture-MS Homo sapiens
26 APLF  
Affinity Capture-MS Homo sapiens
27 CREB1  
Affinity Capture-Western Homo sapiens
28 RBBP4 5928
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
29 PARP2  
Affinity Capture-MS Homo sapiens
30 CLTCL1 8218
Affinity Capture-MS Homo sapiens
31 GINS3  
Affinity Capture-MS Homo sapiens
32 TRIM24  
Co-crystal Structure Homo sapiens
Protein-peptide Homo sapiens
33 HIST1H3E 8353
Affinity Capture-MS Homo sapiens
34 XRCC6 2547
Affinity Capture-MS Homo sapiens
35 XRCC1 7515
Affinity Capture-MS Homo sapiens
36 MMS22L  
Affinity Capture-MS Homo sapiens
37 SUPT6H 6830
Affinity Capture-MS Homo sapiens
38 CHAF1A  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
39 DNAJC9 23234
Two-hybrid Homo sapiens
40 EHMT1  
Affinity Capture-MS Homo sapiens
41 CBX5 23468
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
42 EHMT2 10919
Affinity Capture-MS Homo sapiens
43 HIST1H1A 3024
Affinity Capture-MS Homo sapiens
44 BANF1 8815
Affinity Capture-MS Homo sapiens
45 FBLIM1 54751
Affinity Capture-MS Homo sapiens
46 HIRA  
Affinity Capture-MS Homo sapiens
47 PARP1 142
Affinity Capture-MS Homo sapiens
48 HIST1H2AG 8969
Affinity Capture-MS Homo sapiens
49 H2AFY2 55506
Affinity Capture-MS Homo sapiens
50 RSF1  
Affinity Capture-MS Homo sapiens
51 CHAF1B  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
52 HAT1 8520
Affinity Capture-MS Homo sapiens
53 MCM6 4175
Affinity Capture-MS Homo sapiens
54 CETN2 1069
Affinity Capture-MS Homo sapiens
55 HIST1H1T 3010
Affinity Capture-MS Homo sapiens
56 SPTY2D1  
Affinity Capture-MS Homo sapiens
57 HIST4H4 121504
Affinity Capture-MS Homo sapiens
58 H2AFY 9555
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
59 SUPT16H 11198
Affinity Capture-MS Homo sapiens
60 HMCES  
Affinity Capture-MS Homo sapiens
61 DAXX  
Affinity Capture-MS Homo sapiens
62 HIST2H2AC 8338
Affinity Capture-MS Homo sapiens
63 ITGA4 3676
Affinity Capture-MS Homo sapiens
64 H2AFX 3014
Affinity Capture-MS Homo sapiens
65 HIST2H4A 8370
Affinity Capture-MS Homo sapiens
View the network image/svg+xml
 Pathways in which HIST1H3B is involved
PathwayEvidenceSource
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 TAS Reactome
Activation of anterior HOX genes in hindbrain development during early embryogenesis IEA Reactome
Activation of HOX genes during differentiation IEA Reactome
Amyloid fiber formation TAS Reactome
Assembly of the ORC complex at the origin of replication TAS Reactome
Assembly of the pre-replicative complex TAS Reactome
B-WICH complex positively regulates rRNA expression TAS Reactome
Cell Cycle IEA Reactome
Cell Cycle TAS Reactome
Cell Cycle, Mitotic TAS Reactome
Cellular responses to stimuli TAS Reactome
Cellular responses to stress TAS Reactome
Cellular Senescence TAS Reactome
Chromatin modifications during the maternal to zygotic transition (MZT) IEA Reactome
Chromatin modifying enzymes TAS Reactome
Chromatin modifying enzymes IEA Reactome
Chromatin organization TAS Reactome
Chromatin organization IEA Reactome
Condensation of Prophase Chromosomes TAS Reactome
Cytokine Signaling in Immune system TAS Reactome
Cytokine Signaling in Immune system IEA Reactome
Defective pyroptosis TAS Reactome
Developmental Biology IEA Reactome
Disease TAS Reactome
Diseases of programmed cell death TAS Reactome
DNA methylation IEA Reactome
DNA Replication TAS Reactome
DNA Replication Pre-Initiation TAS Reactome
Epigenetic regulation by WDR5-containing histone modifying complexes IEA Reactome
Epigenetic regulation by WDR5-containing histone modifying complexes TAS Reactome
Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes IEA Reactome
Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes TAS Reactome
Epigenetic regulation of gene expression TAS Reactome
Epigenetic regulation of gene expression IEA Reactome
Epigenetic regulation of gene expression by MLL3 and MLL4 complexes IEA Reactome
Epigenetic regulation of gene expression by MLL3 and MLL4 complexes TAS Reactome
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression IEA Reactome
ESR-mediated signaling TAS Reactome
Estrogen-dependent gene expression TAS Reactome
Factors involved in megakaryocyte development and platelet production TAS Reactome
Formation of the beta-catenin:TCF transactivating complex TAS Reactome
Gene expression (Transcription) TAS Reactome
Gene expression (Transcription) IEA Reactome
Gene Silencing by RNA TAS Reactome
Generic Transcription Pathway TAS Reactome
Generic Transcription Pathway IEA Reactome
HATs acetylate histones TAS Reactome
HATs acetylate histones IEA Reactome
HCMV Early Events TAS Reactome
HCMV Infection TAS Reactome
HCMV Late Events TAS Reactome
HDACs deacetylate histones TAS Reactome
HDMs demethylate histones TAS Reactome
Hemostasis TAS Reactome
Immune System TAS Reactome
Immune System IEA Reactome
Infectious disease TAS Reactome
Interleukin-7 signaling TAS Reactome
Interleukin-7 signaling IEA Reactome
M Phase TAS Reactome
Maternal to zygotic transition (MZT) IEA Reactome
Meiosis IEA Reactome
Meiotic recombination IEA Reactome
Metabolism of proteins TAS Reactome
Mitotic Prophase TAS Reactome
MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis IEA Reactome
MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis TAS Reactome
Negative epigenetic regulation of rRNA expression TAS Reactome
Negative epigenetic regulation of rRNA expression IEA Reactome
NoRC negatively regulates rRNA expression IEA Reactome
NoRC negatively regulates rRNA expression TAS Reactome
Oxidative Stress Induced Senescence TAS Reactome
PKMTs methylate histone lysines TAS Reactome
Positive epigenetic regulation of rRNA expression TAS Reactome
Positive epigenetic regulation of rRNA expression IEA Reactome
PRC2 methylates histones and DNA TAS Reactome
Pre-NOTCH Expression and Processing IEA Reactome
Pre-NOTCH Transcription and Translation IEA Reactome
Regulation of endogenous retroelements TAS Reactome
Regulation of endogenous retroelements IEA Reactome
Regulation of endogenous retroelements by KRAB-ZFP proteins TAS Reactome
Regulation of endogenous retroelements by KRAB-ZFP proteins IEA Reactome
Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) IEA Reactome
Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex TAS Reactome
Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex IEA Reactome
Reproduction IEA Reactome
RHO GTPase Effectors TAS Reactome
RHO GTPases activate PKNs TAS Reactome
RMTs methylate histone arginines TAS Reactome
RNA Polymerase I Promoter Clearance TAS Reactome
RNA Polymerase I Promoter Escape TAS Reactome
RNA Polymerase I Promoter Opening TAS Reactome
RNA Polymerase I Transcription TAS Reactome
RNA Polymerase II Transcription TAS Reactome
RNA Polymerase II Transcription IEA Reactome
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function TAS Reactome
RUNX1 regulates transcription of genes involved in differentiation of HSCs IEA Reactome
Senescence-Associated Secretory Phenotype (SASP) TAS Reactome
Signal Transduction TAS Reactome
Signal Transduction IEA Reactome
Signaling by Interleukins TAS Reactome
Signaling by Interleukins IEA Reactome
Signaling by NOTCH IEA Reactome
Signaling by Nuclear Receptors TAS Reactome
Signaling by Rho GTPases TAS Reactome
Signaling by Rho GTPases, Miro GTPases and RHOBTB3 TAS Reactome
Signaling by WNT TAS Reactome
SIRT1 negatively regulates rRNA expression TAS Reactome
TCF dependent signaling in response to WNT TAS Reactome
Transcriptional regulation by RUNX1 TAS Reactome
Transcriptional regulation by RUNX1 IEA Reactome
Transcriptional regulation by small RNAs TAS Reactome
Transcriptional regulation of granulopoiesis IEA Reactome
Viral Infection Pathways TAS Reactome





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