Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002165
UniProt IDO75151
Primary gene name(s)PHF2
Synonym gene name(s)CENP-35, KIAA0662
Protein nameLysine-specific demethylase PHF2
Protein functionLysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3, H3K9me2, followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3, H3K4me3 at rDNA promoters and promotes expression of rDNA. {ECO:0000269|PubMed:20129925, ECO:0000269|PubMed:21167174, ECO:0000269|PubMed:21532585}.
Subcellular locationNucleus, nucleolus {ECO:0000269|PubMed:20129925}. Chromosome, centromere, kinetochore {ECO:0000269|PubMed:20813266}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: O75151
Gene Ontology
(Biological Process)
Complete annatation
liver development [GO:0001889];
negative regulation of chromatin silencing at rDNA [GO:0061188];
protein demethylation [GO:0006482];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
dioxygenase activity [GO:0051213];
histone demethylase activity [GO:0032452];
histone demethylase activity, H3-K9 specific [GO:0032454];
iron ion binding [GO:0005506];
methylated histone binding [GO:0035064];
zinc ion binding [GO:0008270]
Gene Ontology
(Cellular Component)
Complete annatation
condensed chromosome kinetochore [GO:0000777];
cytoplasm [GO:0005737];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction111272
Phylogenetic treeO75151
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. CD3-0.5741592230585710.08042446627534610.147195817328721
AZA vs. DISU-0.04062839935646520.8738082666991920.991631204917382
AZA vs. IL7-0.1340213460461580.4865157714252080.999311006273513
AZA vs. SAHA-0.557824479127020.04492762753583790.252889864628536
DISU vs. CD30.5214630931128740.1552003986849250.262893674545067
DISU vs. IL7-0.1026142513038320.6866875425988740.917144919347748
DISU vs. SAHA-0.5155606863625720.143264221443960.486620482619319
DMSO vs. AZA-0.009947384622903570.952755137230361
DMSO vs. CD30.5506522138760720.08589174533646930.15093422879901
DMSO vs. DISU0.02828756782309930.9086254046880750.988283279918411
DMSO vs. IL7-0.1164069116955430.5181254384728080.889301967358611
DMSO vs. SAHA-0.5530527197366020.04236257119214040.229491844154115
HIV vs. Mock in Activation0.3195064561019370.6081913673031660.999983755607037
HIV vs. Mock in Latency-0.003146594327365870.9848021784808930.999834320637052
IL7 vs. CD30.4465032626927370.165293807957060.27965804998729
SAHA vs. CD3-0.007651613308799830.9829486928978840.988392393539141
SAHA vs. IL7-0.426795996335780.1138601556995680.310928983154943
(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 unknown
(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
unknown unknown unknown unknown unknown unknown
(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) TRUE
(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 -0.36574 0.00457947
(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
unknown unknown unknown unknown unknown
(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
3KQI X-ray 1.7Å A=1-70.
3PTR X-ray 1.9Å B=60-451.
3PU3 X-ray 1.9Å A/B=60-451.
3PU8 X-ray 1.9Å A/B=60-451.
3PUA X-ray 1.8Å A=60-451.
3PUS X-ray 2.0Å A/B=60-451.

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

HIV Partner Interaction Type PubMed
HIV-1 virus replication enhanced by expression of human gene 18854154

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found