Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001360
UniProt IDQ00839
Primary gene name(s)HNRNPU
Synonym gene name(s)HNRPU, SAFA, U21.1
Protein nameHeterogeneous nuclear ribonucleoprotein U
Protein functionComponent of the CRD-mediated complex that promotes MYC mRNA stabilization. Binds to pre-mRNA. Has high affinity for scaffold-attached region, SAR DNA. Binds to double- and single-stranded DNA and RNA. Plays a role in the circadian regulation of the core clock component ARNTL/BMAL1 transcription, By similarity. {ECO:0000250|UniProtKB:Q8VEK3, ECO:0000269|PubMed:19029303}.
Subcellular locationNucleus {ECO:0000269|PubMed:20858735}. Cytoplasm {ECO:0000269|PubMed:19029303}. Cell surface {ECO:0000269|PubMed:7993898}. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Component of ribonucleosomes. {ECO:0000269|PubMed:17289661}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q00839
Gene Ontology
(Biological Process)
Complete annatation
cardiac muscle cell development [GO:0055013];
cellular response to dexamethasone stimulus [GO:0071549];
circadian regulation of gene expression [GO:0032922];
CRD-mediated mRNA stabilization [GO:0070934];
gene expression [GO:0010467];
mRNA splicing, via spliceosome [GO:0000398];
negative regulation of telomere maintenance via telomerase [GO:0032211];
osteoblast differentiation [GO:0001649];
positive regulation of DNA topoisomerase, ATP-hydrolyzing activity [GO:2000373];
positive regulation of gene expression [GO:0010628];
RNA processing [GO:0006396]
Gene Ontology
(Molecular Function)
Complete annatation
ATP binding [GO:0005524];
core promoter binding [GO:0001047];
DNA binding [GO:0003677];
enhancer binding [GO:0035326];
poly(A RNA binding [GO:0044822];
poly(G binding [GO:0034046];
ribonucleoprotein complex binding [GO:0043021];
RNA binding [GO:0003723];
telomerase RNA binding [GO:0070034]
Gene Ontology
(Cellular Component)
Complete annatation
catalytic step 2 spliceosome [GO:0071013];
cell surface [GO:0009986];
CRD-mediated mRNA stability complex [GO:0070937];
cytoplasmic ribonucleoprotein granule [GO:0036464];
intracellular ribonucleoprotein complex [GO:0030529];
membrane [GO:0016020];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction109433
Phylogenetic treeQ00839
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
      Yes - Two siRNA pools inhibit HIV replication and inhibition of Tat-mediated transactivation of the HIV LTR is not observed
Brass et al., Science, 2008
      unknown
Smith et al., J. Immunol, 2010
      Negatively associated
Interferon-stimulated
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. CD30.9936931885591710.002591762191973990.00829187853055232
AZA vs. DISU-0.300315904279910.2371222208972650.82173184257728
AZA vs. IL70.1381124136244750.4708927738536220.999311006273513
AZA vs. SAHA-0.1503651643297260.5366030547900490.841526679973491
DISU vs. CD3-1.306308276574390.0004157316072942450.00194800691586989
DISU vs. IL70.4290670295976770.09028207828455860.398303286549523
DISU vs. SAHA0.1515066146912360.6051786172041390.875272486353971
DMSO vs. AZA-0.05671899271476030.7337240007753861
DMSO vs. CD3-1.057773745004290.001039562902549360.00354722879431623
DMSO vs. DISU0.2428667227560370.3216876368410950.822644586635435
DMSO vs. IL70.2015711293464350.2605667435184120.762499457035298
DMSO vs. SAHA-0.1011945468412150.6668985645720140.895636095764108
HIV vs. Mock in Activation0.1326351857746070.830919890350780.999983755607037
HIV vs. Mock in Latency0.07934104923086030.6290936731687030.999834320637052
IL7 vs. CD3-0.8486133988980760.00855696422001040.0262046163527462
SAHA vs. CD3-1.168214154898890.001072835357897040.00379967775405602
SAHA vs. IL7-0.291466972221030.230424526322780.471141004759406
(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
-0.4568 0.02148

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
1.8 0.019167184 1.3 0.408752517 1.1 0.843257216
(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 0.513861 0.0420111
(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
1.018 1.063 1.067 1.018 1.002
(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
1ZRJ NMR - A=23-42.

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

HIV Partner Interaction Type PubMed
Rev interacts with 19808671
22174317
Envelope surface glycoprotein gp120 complexes with 23125841
retropepsin cleaves 22944692
Gag-Pol complexes with 23125841
Vpr modulated by 23255807
Pr55(Gag) complexes with 23125841
HIV-1 virus replication enhanced by expression of human gene 18976975
Nef complexes with 23125841

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03040 Spliceosome - Homo sapiens (human)
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