Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000240
UniProt IDQ5T5X7
Primary gene name(s)BEND3
Synonym gene name(s)KIAA1553
Protein nameBEN domain-containing protein 3
Protein functionTranscriptional repressor which associates with the NoRC, nucleolar remodeling complex complex and plays a key role in repressing rDNA transcription. The sumoylated form modulates the stability of the NoRC complex component BAZ2A/TIP5 by controlling its USP21-mediated deubiquitination, PubMed:21914818, PubMed:26100909. Binds to unmethylated major satellite DNA and is involved in the recruitment of the Polycomb repressive complex 2, PRC2 to major satellites, By similarity. {ECO:0000250|UniProtKB:Q6PAL0, ECO:0000269|PubMed:21914818, ECO:0000269|PubMed:26100909}.
Subcellular locationNucleus {ECO:0000269|PubMed:21914818, ECO:0000269|PubMed:25600804}. Nucleus, nucleolus {ECO:0000269|PubMed:26100909}. Note=In the nucleus, observed in heterochromatic foci containing CBX1, CBX3, CBX5 and histone H3 trimethylated at 'Lys-9'. Released from chromatin during decondensation. Association with heterochromatin does not depend on sumoylation. {ECO:0000269|PubMed:21914818}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q5T5X7
Gene Ontology
(Biological Process)
Complete annatation
chromatin silencing at rDNA [GO:0000183];
DNA methylation [GO:0006306];
histone H3-K27 trimethylation [GO:0098532];
histone H3-K4 trimethylation [GO:0080182];
histone H3-K9 trimethylation [GO:0036124];
histone H4 acetylation [GO:0043967];
histone H4-K20 trimethylation [GO:0034773];
negative regulation of transcription from RNA polymerase II promoter [GO:0000122];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
rDNA binding [GO:0000182]
Gene Ontology
(Cellular Component)
Complete annatation
nuclear heterochromatin [GO:0005720];
nucleolus [GO:0005730]
Protein-protein interaction121704
Phylogenetic treeQ5T5X7
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. CD32.888401520498566.66133814775094e-162.54821544575894e-14
AZA vs. DISU0.01427920453490430.9581515792380910.996649735504266
AZA vs. IL70.5362737875380270.01248401419495190.370416429056123
AZA vs. SAHA0.07461969628832470.7787761589332180.941353350035522
DISU vs. CD3-2.887868855275842.87436741075453e-131.12249259973352e-11
DISU vs. IL70.5146179086601050.0540578621404250.30693870876343
DISU vs. SAHA0.06253049236210640.8394065312251570.958240859876863
DMSO vs. AZA0.04931742706170310.8030777811436011
DMSO vs. CD3-2.851136069410763.33066907387547e-161.17234882238163e-14
DMSO vs. DISU0.0334563981615450.8982970483775420.988283279918411
DMSO vs. IL70.4952301110294960.01372897992087520.247269262015763
DMSO vs. SAHA0.01879202793259150.9414706948428080.98612252900613
HIV vs. Mock in Activation0.1251203951742790.8411086798906050.999983755607037
HIV vs. Mock in Latency-0.17639129169650.3737878080952780.999834320637052
IL7 vs. CD3-2.344875985696858.39461833379573e-122.10886803575505e-10
SAHA vs. CD3-2.838187982808341.10689235555128e-133.97163519003757e-12
SAHA vs. IL7-0.4646858224605080.07511125174975420.240628493447173
(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) 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 0.333835 0.0353982
(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
1.006 1.074 0.968 0.867 1.148
(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

not found

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

not found

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found