Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002770
UniProt IDQ96GM5
Primary gene name(s)SMARCD1
Synonym gene name(s)BAF60A
Protein nameSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Protein functionInvolved in chromatin remodeling. Belongs to the neural progenitors-specific chromatin remodeling complex, npBAF complex and the neuron-specific chromatin remodeling complex, nBAF complex. During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes, nBAF. The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth, By similarity. Has a strong influence on vitamin D-mediated transcriptional activity from an enhancer vitamin D receptor element, VDRE. May be a link between mammalian SWI-SNF-like chromatin remodeling complexes and the vitamin D receptor, VDR heterodimer. Mediates critical interactions between nuclear receptors and the BRG1/SMARCA4 chromatin-remodeling complex for transactivation. {ECO:0000250, ECO:0000269|PubMed:12917342, ECO:0000269|PubMed:14698202, ECO:0000269|PubMed:8804307}.
Subcellular locationNucleus {ECO:0000269|PubMed:8804307, ECO:0000305}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q96GM5
Gene Ontology
(Biological Process)
Complete annatation
cellular response to fatty acid [GO:0071398];
chromatin-mediated maintenance of transcription [GO:0048096];
chromatin remodeling [GO:0006338];
covalent chromatin modification [GO:0016569];
nervous system development [GO:0007399];
nucleosome disassembly [GO:0006337];
regulation of transcription from RNA polymerase II promoter [GO:0006357]
Gene Ontology
(Molecular Function)
Complete annatation
chromatin binding [GO:0003682];
protein complex scaffold [GO:0032947];
transcription coactivator activity [GO:0003713]
Gene Ontology
(Cellular Component)
Complete annatation
nBAF complex [GO:0071565];
npBAF complex [GO:0071564];
SWI/SNF complex [GO:0016514]
Protein-protein interaction112486
Phylogenetic treeQ96GM5
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. CD30.7285992609956470.0268634513321110.0593848545728332
AZA vs. DISU0.2323693424656640.3589179625065270.893022876017387
AZA vs. IL70.01216073151327570.9496736550889290.999311006273513
AZA vs. SAHA-0.4156538262661260.09179431131326980.381186624996206
DISU vs. CD3-0.509251246229990.1619728286498370.271467469320396
DISU vs. IL7-0.2294627099996930.3626538784996580.740079868643088
DISU vs. SAHA-0.6457326882278420.02789842096234250.198694397387745
DMSO vs. AZA0.03932622380033080.8149720269679611
DMSO vs. CD3-0.702429335427770.02891762450172890.0609207122246602
DMSO vs. DISU-0.1952711391354970.4238275599346990.87952097606939
DMSO vs. IL7-0.01963588840685570.9132104666874260.982059893733329
DMSO vs. SAHA-0.4600515702595390.05315026546980960.261773742122713
HIV vs. Mock in Activation0.1636723979571820.7923455952529180.999983755607037
HIV vs. Mock in Latency-0.05167733183531930.7546850697113150.999834320637052
IL7 vs. CD3-0.7102036461467360.02803263042016280.0687647777503588
SAHA vs. CD3-1.167853027089310.00126568119955650.0043827701464422
SAHA vs. IL7-0.4304612726878970.07942561499538550.249689618444305
(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 -0.185348 0.188811
(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
0.954 1.027 0.912 0.798 0.992
(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

HIV Partner Interaction Type PubMed
Tat interacts with 19454010

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found