Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000993
UniProt IDQ13868
Primary gene name(s)EXOSC2
Synonym gene name(s)RRP4
Protein nameExosome complex component RRP4
Protein functionNon-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts, PROMPTs, and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination, CSR and/or Ig variable region somatic hypermutation, SHM by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements, AREs within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits, Exo-9 is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC2 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC4 and EXOSC7. {ECO:0000269|PubMed:17545563}.
Subcellular locationCytoplasm. Nucleus, nucleolus. Nucleus.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q13868
Gene Ontology
(Biological Process)
Complete annatation
CUT catabolic process [GO:0071034];
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay [GO:0043928];
exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript, SSU-rRNA, 5.8S rRNA, LSU-rRNA [GO:0000467];
nuclear polyadenylation-dependent rRNA catabolic process [GO:0071035];
nuclear polyadenylation-dependent tRNA catabolic process [GO:0071038];
nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription [GO:0071049];
nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' [GO:0034427];
polyadenylation-dependent snoRNA 3'-end processing [GO:0071051];
positive regulation of cell growth [GO:0030307];
regulation of mRNA stability [GO:0043488];
rRNA processing [GO:0006364];
U4 snRNA 3'-end processing [GO:0034475]
Gene Ontology
(Molecular Function)
Complete annatation
3'-5'-exoribonuclease activity [GO:0000175];
7S RNA binding [GO:0008312]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
cytoplasmic exosome, RNase complex [GO:0000177];
cytosol [GO:0005829];
exosome, RNase complex [GO:0000178];
nuclear exosome, RNase complex [GO:0000176];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction116977
Phylogenetic treeQ13868
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. CD31.440399385372631.59892981979048e-059.40268054774958e-05
AZA vs. DISU-0.2056390541682540.4187316211428490.911342924190573
AZA vs. IL70.3496898089794530.0708700234397170.750344346938375
AZA vs. SAHA-0.2154085423637560.3796355909755740.743971255637779
DISU vs. CD3-1.658678802669238.25679291271975e-066.29872957319521e-05
DISU vs. IL70.5463254833269850.03111685394014950.228265972334673
DISU vs. SAHA-0.008438895749092360.9770015851073780.995922620191181
DMSO vs. AZA0.1033985597054630.5409103718274141
DMSO vs. CD3-1.34866493445833.36542646031113e-050.0001703061794578
DMSO vs. DISU0.3071446094445690.2105688366365860.723830375938263
DMSO vs. IL70.2537289312178610.160787130819370.667061497089279
DMSO vs. SAHA-0.3252817911287190.1698271521617640.497950391095319
HIV vs. Mock in Activation-0.005844263881962380.9925011482569130.999983755607037
HIV vs. Mock in Latency0.007604832960230560.9635920863837830.999834320637052
IL7 vs. CD3-1.083089615204760.0008509002838352760.00369720956421133
SAHA vs. CD3-1.680251305570623.58786755416673e-062.54323443279834e-05
SAHA vs. IL7-0.5687483733083820.0203263888127090.101524183221595
(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 0.246005 0.0884553
(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
1.059 1.01 1.021 0.995 0.959
(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
2NN6 X-ray 3.3Å H=1-293.

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

HIV Partner Interaction Type PubMed
HIV-1 virus replication enhanced by expression of human gene 19460752

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03018 RNA degradation - Homo sapiens (human)