Browse H3F3A

Summary
SymbolH3F3A
NameH3 histone, family 3A
Aliases H3.3A; H3F3
Chromosomal Location1q42.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Nucleus. Chromosome.
Domain PF00125 Core histone H2A/H2B/H3/H4
Function

Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

> Gene Ontology
 
Biological Process GO:0000183 chromatin silencing at rDNA
GO:0001503 ossification
GO:0001558 regulation of cell growth
GO:0001649 osteoblast differentiation
GO:0006323 DNA packaging
GO:0006333 chromatin assembly or disassembly
GO:0006334 nucleosome assembly
GO:0006336 DNA replication-independent nucleosome assembly
GO:0006338 chromatin remodeling
GO:0006342 chromatin silencing
GO:0006997 nucleus organization
GO:0007281 germ cell development
GO:0007283 spermatogenesis
GO:0007286 spermatid development
GO:0007292 female gamete generation
GO:0007338 single fertilization
GO:0007548 sex differentiation
GO:0007565 female pregnancy
GO:0007566 embryo implantation
GO:0007596 blood coagulation
GO:0007599 hemostasis
GO:0008406 gonad development
GO:0008584 male gonad development
GO:0009566 fertilization
GO:0010639 negative regulation of organelle organization
GO:0016049 cell growth
GO:0016458 gene silencing
GO:0022412 cellular process involved in reproduction in multicellular organism
GO:0030261 chromosome condensation
GO:0030307 positive regulation of cell growth
GO:0031047 gene silencing by RNA
GO:0031055 chromatin remodeling at centromere
GO:0031497 chromatin assembly
GO:0031507 heterochromatin assembly
GO:0031508 pericentric heterochromatin assembly
GO:0031509 telomeric heterochromatin assembly
GO:0032200 telomere organization
GO:0033044 regulation of chromosome organization
GO:0034508 centromere complex assembly
GO:0034724 DNA replication-independent nucleosome organization
GO:0034728 nucleosome organization
GO:0035264 multicellular organism growth
GO:0040029 regulation of gene expression, epigenetic
GO:0042692 muscle cell differentiation
GO:0044706 multi-multicellular organism process
GO:0045137 development of primary sexual characteristics
GO:0045814 negative regulation of gene expression, epigenetic
GO:0045815 positive regulation of gene expression, epigenetic
GO:0045927 positive regulation of growth
GO:0046546 development of primary male sexual characteristics
GO:0046661 male sex differentiation
GO:0048232 male gamete generation
GO:0048477 oogenesis
GO:0048515 spermatid differentiation
GO:0048608 reproductive structure development
GO:0050817 coagulation
GO:0050878 regulation of body fluid levels
GO:0060623 regulation of chromosome condensation
GO:0061458 reproductive system development
GO:0065004 protein-DNA complex assembly
GO:0070828 heterochromatin organization
GO:0071103 DNA conformation change
GO:0071824 protein-DNA complex subunit organization
GO:0090230 regulation of centromere complex assembly
GO:1902340 negative regulation of chromosome condensation
GO:2001251 negative regulation of chromosome organization
Molecular Function GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0001046 core promoter sequence-specific DNA binding
GO:0001047 core promoter binding
GO:0001158 enhancer sequence-specific DNA binding
GO:0003682 chromatin binding
GO:0031490 chromatin DNA binding
GO:0031491 nucleosome binding
GO:0031492 nucleosomal DNA binding
GO:0035326 enhancer binding
GO:0042393 histone binding
GO:0043566 structure-specific DNA binding
GO:0046982 protein heterodimerization activity
Cellular Component GO:0000781 chromosome, telomeric region
GO:0000784 nuclear chromosome, telomeric region
GO:0000785 chromatin
GO:0000786 nucleosome
GO:0000788 nuclear nucleosome
GO:0000790 nuclear chromatin
GO:0000803 sex chromosome
GO:0000805 X chromosome
GO:0001740 Barr body
GO:0032993 protein-DNA complex
GO:0044454 nuclear chromosome part
GO:0044815 DNA packaging complex
GO:0098687 chromosomal region
> KEGG and Reactome Pathway
 
KEGG -
Reactome R-HSA-5625886: Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-HSA-5619507: Activation of HOX genes during differentiation
R-HSA-5617472: Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-977225: Amyloid fiber formation
R-HSA-5250924: B-WICH complex positively regulates rRNA expression
R-HSA-1640170: Cell Cycle
R-HSA-69278: Cell Cycle, Mitotic
R-HSA-2559583: Cellular Senescence
R-HSA-2262752: Cellular responses to stress
R-HSA-2299718: Condensation of Prophase Chromosomes
R-HSA-5334118: DNA methylation
R-HSA-1266738: Developmental Biology
R-HSA-427389: ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-212165: Epigenetic regulation of gene expression
R-HSA-983231: Factors involved in megakaryocyte development and platelet production
R-HSA-201722: Formation of the beta-catenin
R-HSA-74160: Gene Expression
R-HSA-211000: Gene Silencing by RNA
R-HSA-109582: Hemostasis
R-HSA-68886: M Phase
R-HSA-1500620: Meiosis
R-HSA-912446: Meiotic recombination
R-HSA-392499: Metabolism of proteins
R-HSA-68875: Mitotic Prophase
R-HSA-5250941: Negative epigenetic regulation of rRNA expression
R-HSA-427413: NoRC negatively regulates rRNA expression
R-HSA-2559580: Oxidative Stress Induced Senescence
R-HSA-212300: PRC2 methylates histones and DNA
R-HSA-5250913: Positive epigenetic regulation of rRNA expression
R-HSA-195258: RHO GTPase Effectors
R-HSA-5625740: RHO GTPases activate PKNs
R-HSA-73777: RNA Polymerase I Chain Elongation
R-HSA-73854: RNA Polymerase I Promoter Clearance
R-HSA-73728: RNA Polymerase I Promoter Opening
R-HSA-73864: RNA Polymerase I Transcription
R-HSA-504046: RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription
R-HSA-427359: SIRT1 negatively regulates rRNA Expression
R-HSA-2559582: Senescence-Associated Secretory Phenotype (SASP)
R-HSA-162582: Signal Transduction
R-HSA-194315: Signaling by Rho GTPases
R-HSA-195721: Signaling by Wnt
R-HSA-201681: TCF dependent signaling in response to WNT
R-HSA-5578749: Transcriptional regulation by small RNAs
Summary
SymbolH3F3A
NameH3 histone, family 3A
Aliases H3.3A; H3F3
Chromosomal Location1q42.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between H3F3A and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 

There is no record.
Summary
SymbolH3F3A
NameH3 histone, family 3A
Aliases H3.3A; H3F3
Chromosomal Location1q42.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of H3F3A in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NS NA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NS NA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NS NA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NS NA/NS
24476824shRNAmelanomaB16Primary screen Total # shRNA with >= 4-fold: 1 Resistant to T-cell proliferation
24476824shRNAmelanomaB16Secondary screen Total # shRNA with >= 4-fold: 2 Resistant to T-cell proliferation
Summary
SymbolH3F3A
NameH3 histone, family 3A
Aliases H3.3A; H3F3
Chromosomal Location1q42.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of H3F3A in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)14120.290.549
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.3750.861
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)870.2270.888
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160.2730.494
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-0.170.926
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.8360.727
729033130MelanomaallAnti-PD-1 (nivolumab) 2623-0.1460.657
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 1511-0.0490.928
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 1112-0.1870.748
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.1120.965
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.1370.974
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.0350.759
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of H3F3A in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 27730001
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27590001
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21170001
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13110001
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 91606.2-6.21
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59011.1-11.11
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38270001
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22130001
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16140001
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolH3F3A
NameH3 histone, family 3A
Aliases H3.3A; H3F3
Chromosomal Location1q42.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of H3F3A. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolH3F3A
NameH3 histone, family 3A
Aliases H3.3A; H3F3
Chromosomal Location1q42.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of H3F3A. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by H3F3A.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolH3F3A
NameH3 histone, family 3A
Aliases H3.3A; H3F3
Chromosomal Location1q42.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of H3F3A. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolH3F3A
NameH3 histone, family 3A
Aliases H3.3A; H3F3
Chromosomal Location1q42.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of H3F3A expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolH3F3A
NameH3 histone, family 3A
Aliases H3.3A; H3F3
Chromosomal Location1q42.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between H3F3A and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolH3F3A
NameH3 histone, family 3A
Aliases H3.3A; H3F3
Chromosomal Location1q42.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting H3F3A collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.