Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000849
UniProt IDQ9UBC3
Primary gene name(s)DNMT3B
Synonym gene name(s)unknown
Protein nameDNA
Protein functionRequired for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing, By similarity. In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1. {ECO:0000250, ECO:0000269|PubMed:16357870, ECO:0000269|PubMed:17303076, ECO:0000269|PubMed:18413740, ECO:0000269|PubMed:18567530}.
Subcellular locationNucleus {ECO:0000269|PubMed:11735126, ECO:0000269|PubMed:12145218}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q9UBC3
Gene Ontology
(Biological Process)
Complete annatation
cellular response to dexamethasone stimulus [GO:0071549];
cellular response to hyperoxia [GO:0071455];
DNA methylation [GO:0006306];
DNA methylation on cytosine within a CG sequence [GO:0010424];
negative regulation of gene expression, epigenetic [GO:0045814];
negative regulation of histone H3-K9 methylation [GO:0051573];
negative regulation of transcription from RNA polymerase II promoter [GO:0000122];
positive regulation of gene expression [GO:0010628];
positive regulation of histone H3-K4 methylation [GO:0051571];
positive regulation of neuron differentiation [GO:0045666];
response to activity [GO:0014823];
response to caffeine [GO:0031000];
response to cocaine [GO:0042220];
response to drug [GO:0042493];
response to estradiol [GO:0032355];
response to hypoxia [GO:0001666];
response to ionizing radiation [GO:0010212];
response to toxic substance [GO:0009636];
response to vitamin A [GO:0033189];
S-adenosylhomocysteine metabolic process [GO:0046498];
S-adenosylmethioninamine metabolic process [GO:0046499]
Gene Ontology
(Molecular Function)
Complete annatation
chromatin binding [GO:0003682];
DNA, cytosine-5--methyltransferase activity [GO:0003886];
DNA, cytosine-5--methyltransferase activity, acting on CpG substrates [GO:0051718];
DNA-methyltransferase activity [GO:0009008];
metal ion binding [GO:0046872];
transcription corepressor activity [GO:0003714];
unmethylated CpG binding [GO:0045322]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
intracellular membrane-bounded organelle [GO:0043231];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction108126
Phylogenetic treeQ9UBC3
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
      unknown
Brass et al., Science, 2008
      unknown
Smith et al., J. Immunol, 2010
      unknown
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. CD30.3920336959240650.3748962210843350.496566995709913
AZA vs. DISU-0.5620794115485930.08554017201685960.612690554939418
AZA vs. IL7-0.1495063396395880.6310028956678380.999311006273513
AZA vs. SAHA0.435009995809510.1153160826852470.432837308365891
DISU vs. CD3-0.9645645942801920.03234768809674660.0761294379969334
DISU vs. IL70.4018531068738920.1978696455860810.572232260270726
DISU vs. SAHA1.000311428358710.001080525866083760.0220658608777078
DMSO vs. AZA-0.06723324339708170.8082624193824191
DMSO vs. CD3-0.4689037373547840.2563979156619210.363166096224788
DMSO vs. DISU0.4932342166357420.07404325367653230.507930210315633
DMSO vs. IL7-0.07482455431811140.7731515616972910.953700815775867
DMSO vs. SAHA0.498003398881650.04623834363666730.241377927588574
HIV vs. Mock in Activation0.726154692818460.3421964658493270.999983755607037
HIV vs. Mock in Latency0.05629139889531870.7540577030216010.999834320637052
IL7 vs. CD3-0.5376302306942740.2159310050466180.341839642860656
SAHA vs. CD30.02141052579368760.9592786296082640.972638696642437
SAHA vs. IL70.5838721666827790.02694019172633170.121804574109995
(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 0.746709 0.000305467
(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
0.894 0.802 1.256 1.302 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
3FLG X-ray 1.8Å A=206-355.
3QKJ X-ray 2.0Å A/B/C/D=206-355.
5CIU X-ray 2.2Å A/B=206-355.

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

HIV Partner Interaction Type PubMed
Tat upregulates 25705251

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa00270 Cysteine and methionine metabolism - Homo sapiens (human)
hsa01100 Metabolic pathways - Homo sapiens (human)
hsa05206 MicroRNAs in cancer - Homo sapiens (human)
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