Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001257
UniProt IDQ13547
Primary gene name(s)HDAC1
Synonym gene name(s)RPD3L1
Protein nameHistone deacetylase 1
Protein functionResponsible for the deacetylation of lysine residues on the N-terminal part of the core histones, H2A, H2B, H3 and H4. Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Deacetylates NR1D2 and abrogates the effect of KAT5-mediated relieving of NR1D2 transcription repression activity. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase, HDAC recruitment, a number of genes implicated in multilineage blood cell development. Involved in CIART-mediated transcriptional repression of the circadian transcriptional activator: CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex or CRY1 through histone deacetylation. {ECO:0000269|PubMed:12837748, ECO:0000269|PubMed:16478997, ECO:0000269|PubMed:17000776, ECO:0000269|PubMed:17704056, ECO:0000269|PubMed:17996965, ECO:0000269|PubMed:19081374, ECO:0000269|PubMed:19343227}.
Subcellular locationNucleus {ECO:0000269|PubMed:10846170}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q13547
Gene Ontology
(Biological Process)
Complete annatation
ATP-dependent chromatin remodeling [GO:0043044];
beta-catenin-TCF complex assembly [GO:1904837];
blood coagulation [GO:0007596];
chromatin organization [GO:0006325];
chromatin remodeling [GO:0006338];
circadian regulation of gene expression [GO:0032922];
embryonic digit morphogenesis [GO:0042733];
epidermal cell differentiation [GO:0009913];
eyelid development in camera-type eye [GO:0061029];
fungiform papilla formation [GO:0061198];
hair follicle placode formation [GO:0060789];
histone deacetylation [GO:0016575];
histone H3 deacetylation [GO:0070932];
histone H4 deacetylation [GO:0070933];
methylation-dependent chromatin silencing [GO:0006346];
negative regulation by host of viral transcription [GO:0043922];
negative regulation of androgen receptor signaling pathway [GO:0060766];
negative regulation of apoptotic process [GO:0043066];
negative regulation of canonical Wnt signaling pathway [GO:0090090];
negative regulation of gene expression [GO:0010629];
negative regulation of transcription, DNA-templated [GO:0045892];
negative regulation of transcription from RNA polymerase II promoter [GO:0000122];
odontogenesis of dentin-containing tooth [GO:0042475];
positive regulation of cell proliferation [GO:0008284];
positive regulation of receptor biosynthetic process [GO:0010870];
positive regulation of transcription, DNA-templated [GO:0045893];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
protein deacetylation [GO:0006476];
regulation of signal transduction by p53 class mediator [GO:1901796];
transcription, DNA-templated [GO:0006351];
viral process [GO:0016032]
Gene Ontology
(Molecular Function)
Complete annatation
activating transcription factor binding [GO:0033613];
core promoter binding [GO:0001047];
deacetylase activity [GO:0019213];
enzyme binding [GO:0019899];
histone deacetylase activity [GO:0004407];
histone deacetylase binding [GO:0042826];
NAD-dependent histone deacetylase activity, H3-K14 specific [GO:0032041];
NF-kappaB binding [GO:0051059];
protein deacetylase activity [GO:0033558];
protein N-terminus binding [GO:0047485];
repressing transcription factor binding [GO:0070491];
RNA polymerase II repressing transcription factor binding [GO:0001103];
RNA polymerase II transcription corepressor activity [GO:0001106];
RNA polymerase II transcription factor binding [GO:0001085];
transcription factor activity, sequence-specific DNA binding [GO:0003700];
transcription factor binding [GO:0008134];
transcription regulatory region DNA binding [GO:0044212];
transcription regulatory region sequence-specific DNA binding [GO:0000976]
Gene Ontology
(Cellular Component)
Complete annatation
chromatin [GO:0000785];
cytoplasm [GO:0005737];
cytosol [GO:0005829];
histone deacetylase complex [GO:0000118];
nuclear chromatin [GO:0000790];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
NuRD complex [GO:0016581];
protein complex [GO:0043234];
Sin3 complex [GO:0016580]
Protein-protein interaction109315
Phylogenetic treeQ13547
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. CD3-0.1981915593930680.5657179090977420.674778436682587
AZA vs. DISU0.2028313027980630.4220330837064180.912833849518076
AZA vs. IL70.02856847446967530.8816730982385310.999311006273513
AZA vs. SAHA0.3010035738891360.2197236935960340.588021914426031
DISU vs. CD30.3877311629710650.2924629855314050.42329208294771
DISU vs. IL7-0.1835220818269070.4655976702347360.805202276094737
DISU vs. SAHA0.1002959165318270.7325913607113750.921843630661778
DMSO vs. AZA0.07592716502958820.6495415659724921
DMSO vs. CD30.2602375950194940.4509764821466050.562833294966333
DMSO vs. DISU-0.1293972062406880.5952679101256380.937098979571498
DMSO vs. IL7-0.03985141701354560.8242665399096980.963051812112721
DMSO vs. SAHA0.2196400310653220.3540974276033380.703521964277433
HIV vs. Mock in Activation0.1241501148358320.8767274821557990.999983755607037
HIV vs. Mock in Latency-0.07258102178179040.6592502834530370.999834320637052
IL7 vs. CD30.2335828520824760.5030158698145020.632663095522182
SAHA vs. CD30.4749588592412660.2457380867440450.3547196328767
SAHA vs. IL70.2696187290413430.2729500126346590.520307217614459
(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
0.2987 0.04998

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 -1.133383799
(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 -0.615521 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
1.024 0.946 0.963 0.928 0.944
(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

Drugbank ID Drug Name Drug Status Pharmacological Action Drug Action
DB02546 Vorinostat approved, investigational yes inhibitor
DB05223 SB939 investigational unknown unknown
DB05651 MGCD-0103 investigational unknown unknown
DB05921 CRA-024781 investigational unknown unknown
DB06176 Romidepsin approved, investigational yes antagonist
DB05015 Belinostat approved, investigational yes inhibitor
DB06603 Panobinostat approved, investigational yes inhibitor

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1TYI Model - A=1-482.
4BKX X-ray 3.0Å B=1-482.
5ICN X-ray 3.3Å B=1-376.

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

HIV Partner Interaction Type PubMed
Vpr cooperates with 19581932
Tat inhibited by 8289393
9371597
10888618
11940654
16838299
20471948
21344388
22077140
23803414
integrase complexes with 19503603
21669392
21669397
Tat induces release of 21344388
HIV-1 virus replication enhanced by expression of human gene 18854154
Tat interacts with 19454010

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa04110 Cell cycle - Homo sapiens (human)
hsa04213 Longevity regulating pathway - multiple species - Homo sapiens (human)
hsa04330 Notch signaling pathway - Homo sapiens (human)
hsa04919 Thyroid hormone signaling pathway - Homo sapiens (human)
hsa05016 Huntington's disease - Homo sapiens (human)
hsa05031 Amphetamine addiction - Homo sapiens (human)
hsa05034 Alcoholism - Homo sapiens (human)
hsa05169 Epstein-Barr virus infection - Homo sapiens (human)
hsa05200 Pathways in cancer - Homo sapiens (human)
hsa05202 Transcriptional misregulation in cancer - Homo sapiens (human)
hsa05203 Viral carcinogenesis - Homo sapiens (human)
hsa05206 MicroRNAs in cancer - Homo sapiens (human)
hsa05220 Chronic myeloid leukemia - Homo sapiens (human)
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