Database ID | HIV0002770 |
UniProt ID | Q96GM5 |
Primary gene name(s) | SMARCD1 |
Synonym gene name(s) | BAF60A |
Protein name | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 |
Protein function | Involved 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 location | Nucleus {ECO:0000269|PubMed:8804307, ECO:0000305}. |
ECO code | Click here for more information. |
Amino acid sequence FASTA format: Q96GM5 |
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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 interaction | 112486 |
Phylogenetic tree | Q96GM5 |
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) |
Up-regulated;
Down-regulated
For brief introduction to each study, please go to the help page.
(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 |
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Experimental Condition | Log2 Fold Change | P value | Adjusted P value |
AZA vs. CD3 | 0.728599260995647 | 0.026863451332111 | 0.0593848545728332 |
AZA vs. DISU | 0.232369342465664 | 0.358917962506527 | 0.893022876017387 |
AZA vs. IL7 | 0.0121607315132757 | 0.949673655088929 | 0.999311006273513 |
AZA vs. SAHA | -0.415653826266126 | 0.0917943113132698 | 0.381186624996206 |
DISU vs. CD3 | -0.50925124622999 | 0.161972828649837 | 0.271467469320396 |
DISU vs. IL7 | -0.229462709999693 | 0.362653878499658 | 0.740079868643088 |
DISU vs. SAHA | -0.645732688227842 | 0.0278984209623425 | 0.198694397387745 |
DMSO vs. AZA | 0.0393262238003308 | 0.814972026967961 | 1 |
DMSO vs. CD3 | -0.70242933542777 | 0.0289176245017289 | 0.0609207122246602 |
DMSO vs. DISU | -0.195271139135497 | 0.423827559934699 | 0.87952097606939 |
DMSO vs. IL7 | -0.0196358884068557 | 0.913210466687426 | 0.982059893733329 |
DMSO vs. SAHA | -0.460051570259539 | 0.0531502654698096 | 0.261773742122713 |
HIV vs. Mock in Activation | 0.163672397957182 | 0.792345595252918 | 0.999983755607037 |
HIV vs. Mock in Latency | -0.0516773318353193 | 0.754685069711315 | 0.999834320637052 |
IL7 vs. CD3 | -0.710203646146736 | 0.0280326304201628 | 0.0687647777503588 |
SAHA vs. CD3 | -1.16785302708931 | 0.0012656811995565 | 0.0043827701464422 |
SAHA vs. IL7 | -0.430461272687897 | 0.0794256149953855 | 0.249689618444305 |
(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 |
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Log2 Fold Change | P Value | ||
unknown | unknown |
(1). Imbeault et al., PloS Pathog., 2012 Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells |
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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) |
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Log2 Fold Change | unknown | ||||
(3). Li et al., J. Immunol., 2013 Lymphatic tissue |
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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 |
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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 |
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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) |
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Log2 Fold Change | P Value | ||||
unknown | unknown |
(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 |
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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 |
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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 |
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Affymetrix Prob ID | Fold Change | In CD8? | Category | |||
unknown | unknown | unknown | unknown |
HIV Partner | Interaction Type | PubMed |
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Tat | interacts with |
19454010 |
Pathway Accession Number | Description | not found |
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