H2AC4 Gene (Protein Coding)

H2A Clustered Histone 4

GC06M026034
GIFtS:
30
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a nucleosome, an octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histon... See more...

Aliases for H2AC4 Gene

Aliases for H2AC4 Gene

  • H2A Clustered Histone 4 2 3 5
  • Histone Cluster 1 H2A Family Member B 2 3
  • H2A Histone Family, Member M 2 3
  • Histone Cluster 1, H2ab 2 3
  • Histone H2A Type 1-B/E 3 4
  • Histone 1, H2ab 2 3
  • Histone H2A/M 3 4
  • HIST1H2AB 3 4
  • H2A/M 2 3
  • H2AFM 3 4
  • Histone H2A.2 4
  • Histone H2A/A 4
  • HIST1H2AE 4
  • H2AC8 3
  • H2AC4 5
  • H2AFA 4

External Ids for H2AC4 Gene

Previous HGNC Symbols for H2AC4 Gene

  • H2AFM
  • HIST1H2AB

Summaries for H2AC4 Gene

Entrez Gene Summary for H2AC4 Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a nucleosome, an octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2A family. Transcripts from this gene lack polyA tails; instead, they contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]

GeneCards Summary for H2AC4 Gene

H2AC4 (H2A Clustered Histone 4) is a Protein Coding gene. Diseases associated with H2AC4 include Alpha-Thalassemia/Mental Retardation Syndrome, X-Linked and Alpha-Thalassemia. Among its related pathways are Cellular Senescence (REACTOME) and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. An important paralog of this gene is H2AC8.

UniProtKB/Swiss-Prot Summary for H2AC4 Gene

  • Core component of nucleosome. 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 Wiki entry for H2AC4 Gene

Additional gene information for H2AC4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2AC4 Gene

Genomics for H2AC4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for H2AC4 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH06J026015 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 0.4 +8.2 8178 20.5 BCLAF1 SP1 ZNF654 ZNF207 NCOR1 MYC IKZF1 ZNF600 SSRP1 JUND H4C2 HSALNG0048725 ABT1 BTN2A2 BTN2A1 HMGN4 BTN2A3P ZNF322 ENSG00000272462 BTN3A2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H2AC4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H2AC4

Genomic Locations for H2AC4 Gene

Latest Assembly
chr6:26,033,092-26,033,618
(GRCh38/hg38)
Size:
527 bases
Orientation:
Minus strand

Previous Assembly
chr6:26,033,320-26,033,846
(GRCh37/hg19 by Entrez Gene)
Size:
527 bases
Orientation:
Minus strand

Genomic View for H2AC4 Gene

Genes around H2AC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2AC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2AC4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for H2AC4 Gene

Proteins for H2AC4 Gene

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  • Protein details for H2AC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P04908-H2A1B_HUMAN
    Recommended name:
    Histone H2A type 1-B/E
    Protein Accession:
    P04908
    Secondary Accessions:
    • P28001
    • Q76P63

    Protein attributes for H2AC4 Gene

    Size:
    130 amino acids
    Molecular mass:
    14135 Da
    Quaternary structure:
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.

    Three dimensional structures from OCA and Proteopedia for H2AC4 Gene

neXtProt entry for H2AC4 Gene

Post-translational modifications for H2AC4 Gene

  • Deiminated on Arg-4 in granulocytes upon calcium entry.
  • Monoubiquitination of Lys-120 (H2AK119Ub) by RING1, TRIM37 and RNF2/RING2 complex gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. It is involved in the initiation of both imprinted and random X inactivation. Ubiquitinated H2A is enriched in inactive X chromosome chromatin. Ubiquitination of H2A functions downstream of methylation of 'Lys-27' of histone H3 (H3K27me). H2AK119Ub by RNF2/RING2 can also be induced by ultraviolet and may be involved in DNA repair. Monoubiquitination of Lys-120 (H2AK119Ub) by TRIM37 may promote transformation of cells in a number of breast cancers (PubMed:25470042). Following DNA double-strand breaks (DSBs), it is ubiquitinated through 'Lys-63' linkage of ubiquitin moieties by the E2 ligase UBE2N and the E3 ligases RNF8 and RNF168, leading to the recruitment of repair proteins to sites of DNA damage. Ubiquitination at Lys-14 and Lys-16 (H2AK13Ub and H2AK15Ub, respectively) in response to DNA damage is initiated by RNF168 that mediates monoubiquitination at these 2 sites, and 'Lys-63'-linked ubiquitin are then conjugated to monoubiquitin; RNF8 is able to extend 'Lys-63'-linked ubiquitin chains in vitro. Deubiquitinated by USP51 at Lys-14 and Lys-16 (H2AK13Ub and H2AK15Ub, respectively) after damaged DNA is repaired (PubMed:27083998). H2AK119Ub and ionizing radiation-induced 'Lys-63'-linked ubiquitination (H2AK13Ub and H2AK15Ub) are distinct events.
  • Phosphorylation on Ser-2 (H2AS1ph) is enhanced during mitosis. Phosphorylation on Ser-2 by RPS6KA5/MSK1 directly represses transcription. Acetylation of H3 inhibits Ser-2 phosphorylation by RPS6KA5/MSK1. Phosphorylation at Thr-121 (H2AT120ph) by DCAF1 is present in the regulatory region of many tumor suppresor genes and down-regulates their transcription.
  • Glutamine methylation at Gln-105 (H2AQ104me) by FBL is specifically dedicated to polymerase I. It is present at 35S ribosomal DNA locus and impairs binding of the FACT complex (PubMed:24352239).
  • Symmetric dimethylation on Arg-4 by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage.
  • Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes.
  • Ubiquitination at Lys16
  • Modification sites at PhosphoSitePlus

Other Protein References for H2AC4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2AC4 Gene

Domains & Families for H2AC4 Gene

Gene Families for H2AC4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for H2AC4 Gene

InterPro:
Blocks:
  • Histone H2A

Suggested Antigen Peptide Sequences for H2AC4 Gene

GenScript: Design optimal peptide antigens:
  • Histone H2A (Q08AJ9_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P04908

UniProtKB/Swiss-Prot:

H2A1B_HUMAN :
  • Belongs to the histone H2A family.
Family:
  • Belongs to the histone H2A family.
genes like me logo Genes that share domains with H2AC4: view

Function for H2AC4 Gene

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Molecular function for H2AC4 Gene

UniProtKB/Swiss-Prot Function:
Core component of nucleosome. 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.

Phenotypes From GWAS Catalog for H2AC4 Gene

Gene Ontology (GO) - Molecular Function for H2AC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA,NAS 6647026
GO:0005515 protein binding IPI 20498094
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2AC4: view
genes like me logo Genes that share phenotypes with H2AC4: view

miRNA for H2AC4 Gene

miRTarBase miRNAs that target H2AC4

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2AC4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H2AC4 Gene

Localization for H2AC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2AC4 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for H2AC4 gene
Compartment Confidence
nucleus 5
extracellular 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endosome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for H2AC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA --
GO:0000786 nucleosome IEA --
GO:0005634 nucleus IEA,IDA 16319397
GO:0005694 chromosome IEA --
GO:0070062 extracellular exosome HDA 19199708
genes like me logo Genes that share ontologies with H2AC4: view

Pathways & Interactions for H2AC4 Gene

PathCards logo

SuperPathways for H2AC4 Gene

SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
DNA methylation
.88
RNA Polymerase I Promoter Opening
.88
B-WICH complex positively regulates rRNA expression
.86
Positive epigenetic regulation of rRNA expression
.86
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
.86
SIRT1 negatively regulates rRNA Expression
.84
NoRC negatively regulates rRNA expression
.83
RNA Polymerase I Chain Elongation
.83
PRC2 methylates histones and DNA
.83
RNA Polymerase I Transcription
.81
Negative epigenetic regulation of rRNA expression
.81
RNA Polymerase I Promoter Clearance
.81
Condensation of Prophase Chromosomes
.78
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
.76
RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription
.75
Epigenetic regulation of gene expression
.73
RHO GTPases activate PKNs
.72
Formation of the beta-catenin-TCF transactivating complex
.64
HDACs deacetylate histones
.60
Amyloid fiber formation
.55
Activation of anterior HOX genes in hindbrain development during early embryogenesis
.50
Activation of HOX genes during differentiation
.50
Systemic lupus erythematosus
.43
RMTs methylate histone arginines
.39
Neutrophil extracellular trap formation
.38
Alcoholism
.35
2 Cellular Senescence (REACTOME)
Cellular Senescence
.64
Oxidative Stress Induced Senescence
.64
Senescence-Associated Secretory Phenotype (SASP)
.56
Cellular responses to stress
.44
3 Chromosome Maintenance
Chromosome Maintenance
.75
Telomere Maintenance
.75
Deposition of new CENPA-containing nucleosomes at the centromere
.66
Nucleosome assembly
.66
4 Cell Cycle, Mitotic
Cell Cycle
.83
Cell Cycle, Mitotic
.83
M Phase
.60
5 Chromatin organization
Chromatin modifying enzymes
.51
Chromatin organization
.51
HATs acetylate histones
.51
genes like me logo Genes that share pathways with H2AC4: view

SIGNOR curated interactions for H2AC4 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for H2AC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006342 chromatin silencing IBA 21873635
GO:0008285 negative regulation of cell proliferation IMP 23956221
genes like me logo Genes that share ontologies with H2AC4: view

Drugs & Compounds for H2AC4 Gene

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(1) Drugs for H2AC4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6959
genes like me logo Genes that share compounds with H2AC4: view

Transcripts for H2AC4 Gene

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mRNA/cDNA for H2AC4 Gene

1 REFSEQ mRNAs :
2 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2AC4

Alternative Splicing Database (ASD) splice patterns (SP) for H2AC4 Gene

No ASD Table

Relevant External Links for H2AC4 Gene

GeneLoc Exon Structure for
H2AC4

Expression for H2AC4 Gene

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  1. Primer products for research

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H2AC4

SOURCE GeneReport for Unigene cluster for H2AC4 Gene:

Hs.248174

Evidence on tissue expression from TISSUES for H2AC4 Gene

  • Liver(4.3)
No Expression Related Data Available

Primer products for research

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for H2AC4 Gene

Orthologs for H2AC4 Gene

This gene was present in the common ancestor of mammals.

Orthologs for H2AC4 Gene

Organism Taxonomy Gene Similarity Type Details
Mouse
(Mus musculus)
 Mammalia Hist1h2ag 29
  • 85.9 (n)
H2ac11 16
Cow
(Bos Taurus)
 Mammalia LOC524236 29
  • 84.87 (n)
Chimpanzee
(Pan troglodytes)
 Mammalia LOC471884 29
  • 83.08 (n)
Rat
(Rattus norvegicus)
 Mammalia Hist1h2ak 29
  • 82.82 (n)
Species where no ortholog for H2AC4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for H2AC4 Gene

ENSEMBL:
Gene Tree for H2AC4 (if available)
TreeFam:
Gene Tree for H2AC4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2AC4: view image
Alliance of Genome Resources:
Additional Orthologs for H2AC4

Paralogs for H2AC4 Gene

Variants for H2AC4 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for H2AC4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for H2AC4 Gene

Variant ID Type Subtype PubMed ID
dgv5926n100 CNV gain 25217958
esv3608392 CNV gain 21293372
nsv1023453 CNV gain 25217958
nsv1026692 CNV loss 25217958
nsv428137 CNV loss 18775914
nsv509122 CNV insertion 20534489

Variation tolerance for H2AC4 Gene

Residual Variation Intolerance Score: 31% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.94; 19.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H2AC4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2AC4
Leiden Open Variation Database (LOVD)
H2AC4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for H2AC4 Gene

Disorders for H2AC4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for H2AC4 Gene - From: GCD

Disorder Aliases PubMed IDs
alpha-thalassemia/mental retardation syndrome, x-linked
  • atrx
alpha-thalassemia
  • thalassemia, alpha-
- elite association - COSMIC cancer census association via MalaCards
Search H2AC4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for H2AC4

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with H2AC4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for H2AC4 Gene

Publications for H2AC4 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4
  2. The human histone gene cluster at the D6S105 locus. (PMID: 9439656) Albig W … Doenecke D (Human genetics 1997) 2 3 4
  3. Precise characterization of human histones in the H2A gene family by top down mass spectrometry. (PMID: 16457589) Boyne MT … Kelleher NL (Journal of proteome research 2006) 3 4
  4. DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A. (PMID: 16702407) Bergink S … Dantuma NP (Genes & development 2006) 3 4
  5. Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes. (PMID: 15823041) Hagiwara T … Yamada M (Biochemistry 2005) 3 4

ExternalLinks

View latest publications for H2AC4 gene in Mastermind

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