Protein Information (annotations from UniProt)
| 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 |
|
| 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) |
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 |
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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 | ||
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 |
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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 | ||||
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 |
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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 | |||
Protein Overview top
Drug-protein Interaction (annotations from DrugBank) top
Protein Secondary Structure (annotations from PDB) top
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 |
|---|