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H2AFX (H2A histone family, member X)

Written2009-03Niloo Srivastava, Sailesh Gochhait, P Kalaiarasan, Rameshwar NK Bamezai
National center of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India

(Note : for Links provided by Atlas : click)

Identity

Alias_namesH2AX
H2A histone family
Other aliasH2A.X
H2A/X
H2a/x
HGNC (Hugo) H2AFX
LocusID (NCBI) 3014
Atlas_Id 40783
Location 11q23.3  [Link to chromosome band 11q23]
Location_base_pair Starts at 119093875 and ends at 119095467 bp from pter ( according to hg19-Feb_2009)  [Mapping H2AFX.png]
Local_order According to NCBI Map Viewer, genes from centromere to telomere direction with respect to H2AFX, on 11q23 are: hypoxia up-regulated 1 (HYOU1), vacuolar protein sorting 11 homolog (S. cerevisiae) (VPS11), hydroxymethylbilane synthase (HMBS), H2A histone family, member X (H2AFX), dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase) (DPAGT1), transmembrane protein 24 (TMEM 24), MBD2-interacting zinc finger (MIZF).
Fusion genes
(updated 2016)
H2AFX (11q23.3) / ATG12 (5q22.3)WDR18 (19p13.3) / H2AFX (11q23.3)
Note Histone H2AX is a variant of histone H2A and it constitutes ~ 15-20% of total histone H2A pool. It differs from H2A in the presence of evolutionary conserved C-terminal tail that gets phosphorylated at serine 140 residue in response to genomic insult and also in response to certain stress (heat, hypoxia and changes in osmolarity).

DNA/RNA

Note H2AFX gene sequence is highly GC rich and lies in the CpG island (118470228-11847164) with a ratio of observed to expected CpG 1.02.
 
  Figure 1: Gene Structure of H2AFX.
Description According to Entrez-Gene, H2AFX gene maps to NC 000011.8 in the region between 118469794 and 118471387 on the minus strand. It is a small gene (DQ015918) having a single exon of 432 nucleotides, 73 bp 5'UTR and 1089 bp 3'UTR. It contains no introns.
H2AFX is recognized as an important DNA damage response (DDR) gene. It maps to cytogenetic locus 11q23.2-23.3 that is highly represented among those commonly deleted or translocated in several haematological malignancies or solid tumors. Interestingly other key DNA damage response genes in the region are ATM, MRE11 and CHK1; combined loss of which can be detrimental to the cell.
Transcription Histone H2AFX mRNA (NM_002105) has 1594 bp and is synthesized in G1 as well as S phase. It is known to have two forms of transcript; one having a polyA tail (1651 bp) and another having a conserved stem-loop and U7 binding sequences involved in the processing and stability of replication type histone mRNAs (575 bp).
Pseudogene No pseudogene for H2AFX is known.

Protein

Note The C-terminal tail of H2AX is highly conserved along with the SQ-motif that gets phosphorylated at the serine residue by members of phosphoinositide 3-kinase related protein kinases (PIKKs).
 
  Figure 2 : Protein Structure of histone H2AX protein.
Description A single exon having a length of 432 nucleotides codes for H2AX protein of molecular weight 15 kDA. It has a characteristic histone H2A domain ranging from 18 to 91 amino acid with H2A signature motif from 22-28 aa. The SQ-motif (140-141) is a feature of H2AX variant that differentiates it from rest of the members of H2A family. The H2AX protein undergoes several posttranslational modifications either in constitutive manner like monoubiquitination at lysine 120 or in response to cellular stress/DNA damage, like acetylation of lysine 5 and phosphorylation of serine 140 and tyrosine 143 residues. By virtue of these posttranslational events, H2AX acquires new regulatory functions during DNA repair and other metabolic processes.
Expression H2AX is ubiquitously expressed in humans with the highest levels observed in the proliferating tissues, eg., testis and thymus. Phosphorylated H2AX is widely correlated with the extent of DNA damage and forms discrete nuclear foci at the sites of damage.
Localisation Located in the nucleus and forms discrete foci upon DNA damage.
The figure 3 shows typical staining of H2AX and gamma H2AX in HeLa cells before and after the treatment with etoposide (10mM).
 
  Figure 3
Function Phosphorylation of Ser-140 (known as gamma-H2AX) is critical during DNA double-strand break signaling. Apart from the exogeneous agents (radiation and chemicals), DSBs generated during replication fork stalling, meiotic recombination events and during immunoglobulin class switching in lymphocytes are also known to induce the formation of gamma H2AX. This phosphorylation event can extend up to 1 megabase on either side of DSB, amplifying the damage signal and hence facilitating recruitment of repair proteins and accomplishment of repair process. The kinases responsible for the serine phosphorylation are ATM, ATR and DNA-PKcs. Once the repair is complete, dephosphorylation of Ser-140 is mediated by a phosphatase, PP2A.
During meiosis, programmed DSBs are formed in SPO-11 dependent manner and H2AX-Ser-140 phosphorylation has been shown to accumulate at synaptonemal complexes. With the progression from leptotene to zygotene and pachytene, the gamma H2AX is subsequently seen sequestered at unsynapsed regions of autosomes and also in the XY-body, probably required for meiotic sex chromosome inactivation. (MSCI).
Apart from ser-140 phosphorylation, the protein also gets modified at lysine 5 residue by TIP60 mediated acetylation and subsequent ubiquitination by UBC-13 in response to DNA damage. The functional implication of this modification is not very clear although it is suggested that this helps in chromatin modulation during the repair process.
Tyrosine 143 phosphorylation of H2AX by WSTF having a tyrosine kinase activity and a component of WICH ATP-dependent chromatin remodeling complex was recently shown to be critical during DNA damage response and acts as a switch to apoptosis/cell survival.
No mutation in H2AFX gene has been detected so far. Few direct studies on human cancers, one on 101 familial breast cancer samples, another on 112 tumors from seven different B cell leukemia/lymphoma and yet another on sporadic breast cancer patients failed to identify any change at nucleotide level. A partial deletion of the region encompassing H2AFX was however identified in significant proportion of head and neck squamous cell carcinoma.
Homology The sequence of 22 residues at carboxy terminal of H2AX is unique and is unrelated to any of the H2A family member but is highly conserved and is present in all eukaryotes.

Mutations

Note No mutation so far has been reported for H2AFX.

Implicated in

Note
  
Entity Various cancers
Note Histone H2AX has been implicated in different human cancers based on association studies of polymorphisms found in the promoter region of the gene. SNPs in the far promoter region of H2AFX (rs643788, rs8551 and rs7759, rs2509049) has been shown to be associated with the risk of sporadic breast cancer and Non-Hodgkin's Lymphomas but no association was observed in case of bladder carcinoma. Also alteration of H2AFX gene copy number in significant proportion (37%) of sporadic breast cancer patients has been reported.
  

Bibliography

DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis.
Bartkova J, Horejsi Z, Koed K, Kramer A, Tort F, Zieger K, Guldberg P, Sehested M, Nesland JM, Lukas C, Orntoft T, Lukas J, Bartek J.
Nature. 2005 Apr 14;434(7035):864-70.
PMID 15829956
 
Histone H2AX: a dosage-dependent suppressor of oncogenic translocations and tumors.
Bassing CH, Suh H, Ferguson DO, Chua KF, Manis J, Eckersdorff M, Gleason M, Bronson R, Lee C, Alt FW.
Cell. 2003 Aug 8;114(3):359-70.
PMID 12914700
 
H2AX haploinsufficiency modifies genomic stability and tumor susceptibility.
Celeste A, Difilippantonio S, Difilippantonio MJ, Fernandez-Capetillo O, Pilch DR, Sedelnikova OA, Eckhaus M, Ried T, Bonner WM, Nussenzweig A.
Cell. 2003 Aug 8;114(3):371-83.
PMID 12914701
 
Genomic instability in mice lacking histone H2AX.
Celeste A, Petersen S, Romanienko PJ, Fernandez-Capetillo O, Chen HT, Sedelnikova OA, Reina-San-Martin B, Coppola V, Meffre E, Difilippantonio MJ, Redon C, Pilch DR, Olaru A, Eckhaus M, Camerini-Otero RD, Tessarollo L, Livak F, Manova K, Bonner WM, Nussenzweig MC, Nussenzweig A.
Science. 2002 May 3;296(5569):922-7. Epub 2002 Apr 4.
PMID 11934988
 
Response to RAG-mediated VDJ cleavage by NBS1 and gamma-H2AX.
Chen HT, Bhandoola A, Difilippantonio MJ, Zhu J, Brown MJ, Tai X, Rogakou EP, Brotz TM, Bonner WM, Ried T, Nussenzweig A.
Science. 2000 Dec 8;290(5498):1962-5.
PMID 11110662
 
Analysis of variants in DNA damage signalling genes in bladder cancer.
Choudhury A, Elliott F, Iles MM, Churchman M, Bristow RG, Bishop DT, Kiltie AE.
BMC Med Genet. 2008 Jul 18;9:69.
PMID 18638378
 
gamma-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repair.
Chowdhury D, Keogh MC, Ishii H, Peterson CL, Buratowski S, Lieberman J.
Mol Cell. 2005 Dec 9;20(5):801-9. Epub 2005 Nov 28.
PMID 16310392
 
Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions.
Cook PJ, Ju BG, Telese F, Wang X, Glass CK, Rosenfeld MG.
Nature. 2009 Apr 2;458(7238):591-6. Epub 2009 Feb 22.
PMID 19234442
 
Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions.
Gorgoulis VG, Vassiliou LV, Karakaidos P, Zacharatos P, Kotsinas A, Liloglou T, Venere M, Ditullio RA Jr, Kastrinakis NG, Levy B, Kletsas D, Yoneta A, Herlyn M, Kittas C, Halazonetis TD.
Nature. 2005 Apr 14;434(7035):907-13.
PMID 15829965
 
A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery.
Keogh MC, Kim JA, Downey M, Fillingham J, Chowdhury D, Harrison JC, Onishi M, Datta N, Galicia S, Emili A, Lieberman J, Shen X, Buratowski S, Haber JE, Durocher D, Greenblatt JF, Krogan NJ.
Nature. 2006 Jan 26;439(7075):497-501. Epub 2005 Nov 20.
PMID 16299494
 
Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions.
Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates JR 3rd, Abmayr SM, Washburn MP, Workman JL.
Science. 2004 Dec 17;306(5704):2084-7. Epub 2004 Nov 4.
PMID 15528408
 
Genetic variants in the H2AFX promoter region are associated with risk of sporadic breast cancer in non-Hispanic white women aged
Lu J, Wei Q, Bondy ML, Brewster AM, Bevers TB, Yu TK, Buchholz TA, Meric-Bernstam F, Hunt KK, Singletary SE, Wang LE.
Breast Cancer Res Treat. 2008 Jul;110(2):357-66. Epub 2007 Sep 13.
PMID 17851762
 
Recombinational DNA double-strand breaks in mice precede synapsis.
Mahadevaiah SK, Turner JM, Baudat F, Rogakou EP, de Boer P, Blanco-Rodriguez J, Jasin M, Keeney S, Bonner WM, Burgoyne PS.
Nat Genet. 2001 Mar;27(3):271-6.
PMID 11242108
 
Absence of constitutional H2AX gene mutations in 101 hereditary breast cancer families.
Monteiro AN, Zhang S, Phelan CM, Narod SA.
J Med Genet. 2003 Apr;40(4):e51.
PMID 12676924
 
Genetic variation in H2AFX contributes to risk of non-Hodgkin lymphoma.
Novik KL, Spinelli JJ, Macarthur AC, Shumansky K, Sipahimalani P, Leach S, Lai A, Connors JM, Gascoyne RD, Gallagher RP, Brooks-Wilson AR.
Cancer Epidemiol Biomarkers Prev. 2007 Jun;16(6):1098-106.
PMID 17548670
 
Loss of distal 11q is associated with DNA repair deficiency and reduced sensitivity to ionizing radiation in head and neck squamous cell carcinoma.
Parikh RA, White JS, Huang X, Schoppy DW, Baysal BE, Baskaran R, Bakkenist CJ, Saunders WS, Hsu LC, Romkes M, Gollin SM.
Genes Chromosomes Cancer. 2007 Aug;46(8):761-75.
PMID 17492757
 
DNA-PK is responsible for enhanced phosphorylation of histone H2AX under hypertonic conditions.
Reitsema T, Klokov D, Banath JP, Olive PL.
DNA Repair (Amst). 2005 Sep 28;4(10):1172-81.
PMID 16046194
 
Megabase chromatin domains involved in DNA double-strand breaks in vivo.
Rogakou EP, Boon C, Redon C, Bonner WM.
J Cell Biol. 1999 Sep 6;146(5):905-16.
PMID 10477747
 
Role of H2AX in DNA damage response and human cancers.
Srivastava N, Gochhait S, de Boer P, Bamezai RN.
Mutat Res. 2009 Mar-Jun;681(2-3):180-8. Epub 2008 Aug 29.
PMID 18804552
 
Absence of H2AX gene mutations in B-cell leukemias and lymphomas.
Walsh SH, Rosenquist R.
Leukemia. 2005 Mar;19(3):464.
PMID 15674416
 
WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity.
Xiao A, Li H, Shechter D, Ahn SH, Fabrizio LA, Erdjument-Bromage H, Ishibe-Murakami S, Wang B, Tempst P, Hofmann K, Patel DJ, Elledge SJ, Allis CD.
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PMID 19092802
 

Citation

This paper should be referenced as such :
Srivastava, N ; Gochhait, S ; Kalaiarasan, P ; Bamezai, RNK
H2AFX (H2A histone family, member X)
Atlas Genet Cytogenet Oncol Haematol. 2010;14(2):117-120.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/H2AFXID40783ch11q23.html


External links

Nomenclature
HGNC (Hugo)H2AFX   4739
Cards
AtlasH2AFXID40783ch11q23
Entrez_Gene (NCBI)H2AFX  3014  H2A histone family member X
AliasesH2A.X; H2A/X; H2AX
GeneCards (Weizmann)H2AFX
Ensembl hg19 (Hinxton)ENSG00000188486 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000188486 [Gene_View]  chr11:119093875-119095467 [Contig_View]  H2AFX [Vega]
ICGC DataPortalENSG00000188486
TCGA cBioPortalH2AFX
AceView (NCBI)H2AFX
Genatlas (Paris)H2AFX
WikiGenes3014
SOURCE (Princeton)H2AFX
Genetics Home Reference (NIH)H2AFX
Genomic and cartography
GoldenPath hg38 (UCSC)H2AFX  -     chr11:119093875-119095467 -  11q23.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)H2AFX  -     11q23.3   [Description]    (hg19-Feb_2009)
EnsemblH2AFX - 11q23.3 [CytoView hg19]  H2AFX - 11q23.3 [CytoView hg38]
Mapping of homologs : NCBIH2AFX [Mapview hg19]  H2AFX [Mapview hg38]
OMIM601772   
Gene and transcription
Genbank (Entrez)BC004915 BC011694 BC013416 CR457079 X14850
RefSeq transcript (Entrez)NM_002105
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)H2AFX
Cluster EST : UnigeneHs.477879 [ NCBI ]
CGAP (NCI)Hs.477879
Alternative Splicing GalleryENSG00000188486
Gene ExpressionH2AFX [ NCBI-GEO ]   H2AFX [ EBI - ARRAY_EXPRESS ]   H2AFX [ SEEK ]   H2AFX [ MEM ]
Gene Expression Viewer (FireBrowse)H2AFX [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3014
GTEX Portal (Tissue expression)H2AFX
Protein : pattern, domain, 3D structure
UniProt/SwissProtP16104   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP16104  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP16104
Splice isoforms : SwissVarP16104
PhosPhoSitePlusP16104
Domaine pattern : Prosite (Expaxy)HISTONE_H2A (PS00046)   
Domains : Interpro (EBI)Histone-fold    Histone_H2A    Histone_H2A/H2B/H3    Histone_H2A_C    Histone_H2A_CS   
Domain families : Pfam (Sanger)Histone (PF00125)    Histone_H2A_C (PF16211)   
Domain families : Pfam (NCBI)pfam00125    pfam16211   
Domain families : Smart (EMBL)H2A (SM00414)  
Conserved Domain (NCBI)H2AFX
DMDM Disease mutations3014
Blocks (Seattle)H2AFX
PDB (SRS)1YDP    2AZM    2D31    2DYP    3SHV    3SQD    3SZM    3U3Z   
PDB (PDBSum)1YDP    2AZM    2D31    2DYP    3SHV    3SQD    3SZM    3U3Z   
PDB (IMB)1YDP    2AZM    2D31    2DYP    3SHV    3SQD    3SZM    3U3Z   
PDB (RSDB)1YDP    2AZM    2D31    2DYP    3SHV    3SQD    3SZM    3U3Z   
Structural Biology KnowledgeBase1YDP    2AZM    2D31    2DYP    3SHV    3SQD    3SZM    3U3Z   
SCOP (Structural Classification of Proteins)1YDP    2AZM    2D31    2DYP    3SHV    3SQD    3SZM    3U3Z   
CATH (Classification of proteins structures)1YDP    2AZM    2D31    2DYP    3SHV    3SQD    3SZM    3U3Z   
SuperfamilyP16104
Human Protein AtlasENSG00000188486
Peptide AtlasP16104
HPRD03465
IPIIPI00219037   
Protein Interaction databases
DIP (DOE-UCLA)P16104
IntAct (EBI)P16104
FunCoupENSG00000188486
BioGRIDH2AFX
STRING (EMBL)H2AFX
ZODIACH2AFX
Ontologies - Pathways
QuickGOP16104
Ontology : AmiGODNA damage checkpoint  double-strand break repair via homologous recombination  chromosome, telomeric region  nucleosome  nuclear chromatin  condensed nuclear chromosome  male germ cell nucleus  XY body  DNA binding  DNA binding  damaged DNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  replication fork  double-strand break repair  double-strand break repair via nonhomologous end joining  nucleosome assembly  chromatin silencing  cellular response to DNA damage stimulus  spermatogenesis  response to ionizing radiation  viral process  nuclear speck  enzyme binding  cerebral cortex development  site of double-strand break  histone binding  positive regulation of DNA repair  protein heterodimerization activity  meiotic cell cycle  extracellular exosome  cellular response to gamma radiation  cellular senescence  
Ontology : EGO-EBIDNA damage checkpoint  double-strand break repair via homologous recombination  chromosome, telomeric region  nucleosome  nuclear chromatin  condensed nuclear chromosome  male germ cell nucleus  XY body  DNA binding  DNA binding  damaged DNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  replication fork  double-strand break repair  double-strand break repair via nonhomologous end joining  nucleosome assembly  chromatin silencing  cellular response to DNA damage stimulus  spermatogenesis  response to ionizing radiation  viral process  nuclear speck  enzyme binding  cerebral cortex development  site of double-strand break  histone binding  positive regulation of DNA repair  protein heterodimerization activity  meiotic cell cycle  extracellular exosome  cellular response to gamma radiation  cellular senescence  
Pathways : KEGGAlcoholism    Systemic lupus erythematosus   
REACTOMEP16104 [protein]
REACTOME PathwaysR-HSA-977225 [pathway]   
NDEx NetworkH2AFX
Atlas of Cancer Signalling NetworkH2AFX
Wikipedia pathwaysH2AFX
Orthology - Evolution
OrthoDB3014
GeneTree (enSembl)ENSG00000188486
Phylogenetic Trees/Animal Genes : TreeFamH2AFX
HOVERGENP16104
HOGENOMP16104
Homologs : HomoloGeneH2AFX
Homology/Alignments : Family Browser (UCSC)H2AFX
Gene fusions - Rearrangements
Fusion : MitelmanWDR18/H2AFX [19p13.3/11q23.3]  [t(11;19)(q23;p13)]  
Fusion: TCGAWDR18 19p13.3 H2AFX 11q23.3 LAML
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerH2AFX [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)H2AFX
dbVarH2AFX
ClinVarH2AFX
1000_GenomesH2AFX 
Exome Variant ServerH2AFX
ExAC (Exome Aggregation Consortium)H2AFX (select the gene name)
Genetic variants : HAPMAP3014
Genomic Variants (DGV)H2AFX [DGVbeta]
DECIPHERH2AFX [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisH2AFX 
Mutations
ICGC Data PortalH2AFX 
TCGA Data PortalH2AFX 
Broad Tumor PortalH2AFX
OASIS PortalH2AFX [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICH2AFX  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDH2AFX
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch H2AFX
DgiDB (Drug Gene Interaction Database)H2AFX
DoCM (Curated mutations)H2AFX (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)H2AFX (select a term)
intoGenH2AFX
NCG5 (London)H2AFX
Cancer3DH2AFX(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601772   
Orphanet
MedgenH2AFX
Genetic Testing Registry H2AFX
NextProtP16104 [Medical]
TSGene3014
GENETestsH2AFX
Target ValidationH2AFX
Huge Navigator H2AFX [HugePedia]
snp3D : Map Gene to Disease3014
BioCentury BCIQH2AFX
ClinGenH2AFX
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3014
Chemical/Pharm GKB GenePA29116
Clinical trialH2AFX
Miscellaneous
canSAR (ICR)H2AFX (select the gene name)
Probes
Litterature
PubMed358 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineH2AFX
EVEXH2AFX
GoPubMedH2AFX
iHOPH2AFX
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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