Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001241
UniProt IDP16104
Primary gene name(s)H2AFX
Synonym gene name(s)H2AX
Protein nameHistone H2AX
Protein functionVariant histone H2A which replaces conventional H2A in a subset of nucleosomes. 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. Required for checkpoint-mediated arrest of cell cycle progression in response to low doses of ionizing radiation and for efficient repair of DNA double strand breaks, DSBs specifically when modified by C-terminal phosphorylation. {ECO:0000269|PubMed:10959836, ECO:0000269|PubMed:12419185, ECO:0000269|PubMed:12607005, ECO:0000269|PubMed:15201865}.
Subcellular locationNucleus {ECO:0000269|PubMed:12419185, ECO:0000269|PubMed:12660252, ECO:0000269|PubMed:12697768, ECO:0000269|PubMed:15613478, ECO:0000269|PubMed:24429368}. Chromosome {ECO:0000269|PubMed:10959836, ECO:0000269|PubMed:11673449, ECO:0000269|PubMed:12607005, ECO:0000269|PubMed:12660252, ECO:0000269|PubMed:15059890, ECO:0000269|PubMed:15201865, ECO:0000269|PubMed:15613478}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P16104
Gene Ontology
(Biological Process)
Complete annatation
cellular response to DNA damage stimulus [GO:0006974];
cellular response to gamma radiation [GO:0071480];
cellular senescence [GO:0090398];
cerebral cortex development [GO:0021987];
chromatin silencing [GO:0006342];
DNA damage checkpoint [GO:0000077];
double-strand break repair [GO:0006302];
double-strand break repair via homologous recombination [GO:0000724];
double-strand break repair via nonhomologous end joining [GO:0006303];
meiotic cell cycle [GO:0051321];
nucleosome assembly [GO:0006334];
positive regulation of DNA repair [GO:0045739];
response to ionizing radiation [GO:0010212];
spermatogenesis [GO:0007283];
viral process [GO:0016032]
Gene Ontology
(Molecular Function)
Complete annatation
damaged DNA binding [GO:0003684];
DNA binding [GO:0003677];
enzyme binding [GO:0019899];
histone binding [GO:0042393]
Gene Ontology
(Cellular Component)
Complete annatation
condensed nuclear chromosome [GO:0000794];
extracellular exosome [GO:0070062];
male germ cell nucleus [GO:0001673];
nuclear chromatin [GO:0000790];
nucleoplasm [GO:0005654];
nucleosome [GO:0000786];
nucleus [GO:0005634];
replication fork [GO:0005657];
site of double-strand break [GO:0035861];
XY body [GO:0001741]
Protein-protein interaction109268
Phylogenetic treeP16104
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: unknown
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model

DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD31.214485258192210.0002677787294245170.00114658327739634
AZA vs. DISU-0.02049358096310420.9361897660476940.99506396880143
AZA vs. IL7-0.1069462411355890.6725194803234910.999311006273513
AZA vs. SAHA-0.35552017046880.1539297764288590.500504195403067
DISU vs. CD3-1.246426296245010.0007174086464903920.00310283467524883
DISU vs. IL7-0.09653624644812030.7309830158733010.932983648383965
DISU vs. SAHA-0.3327929515003060.2595179438294610.637018739322796
DMSO vs. AZA-0.2322775507589290.1800963863671941
DMSO vs. CD3-1.457855734575068.42619419716417e-064.92590669694522e-05
DMSO vs. DISU-0.2139309438024940.3868072708814280.860054371264532
DMSO vs. IL70.1331184805667160.5713544853305840.90371475916411
DMSO vs. SAHA-0.1283579417025450.5939931136861410.862268369905975
HIV vs. Mock in Activation0.4435097028774110.4913352896310820.999983755607037
HIV vs. Mock in Latency-0.1422859292990750.6185883207016150.999834320637052
IL7 vs. CD3-1.316558851150888.08248406731771e-050.000483633514675188
SAHA vs. CD3-1.593418168713941.16543232991928e-057.17152519880913e-05
SAHA vs. IL7-0.2514382988697660.3150147393336560.563958691296381
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
unknown unknown

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander unknown unknown unknown
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change -1.018574052
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
2.2 0.000236499 1.5 0.016205788 1.8 0.153491672
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) FALSE
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK 0.393572 0.00261319
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
0.974 0.782 0.848 0.937 0.818
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
unknown unknown unknown unknown

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1YDP X-ray 1.9Å P=78-86.
2AZM X-ray 2.4Å C/D=134-143.
2D31 X-ray 3.2Å C/F=78-86.
2DYP X-ray 2.5Å C=78-86.
3SHV X-ray 2.1Å C/D=134-143.
3SQD X-ray 2.1Å C/D=134-143.
3SZM X-ray 2.6Å I/J/K/L/M/N/O/P=134-143.
3U3Z X-ray 1.5Å B=140-143.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

HIV Partner Interaction Type PubMed
Vpr interacts with 23726848
integrase induces phosphorylation of 23739328
Vpr induces phosphorylation of 15485898
Tat binds 9566873
Vpr activates 19657269

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa05034 Alcoholism - Homo sapiens (human)
hsa05322 Systemic lupus erythematosus - Homo sapiens (human)