Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002568
UniProt IDQ92541
Primary gene name(s)RTF1
Synonym gene name(s)KIAA0252
Protein nameRNA polymerase-associated protein RTF1 homolog
Protein functionComponent of the PAF1 complex, PAF1C which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4', H3K4me3. PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B, H2BK120ub1; UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Binds single-stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4', H3K4me3 on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex, By similarity. {ECO:0000250, ECO:0000269|PubMed:19345177, ECO:0000269|PubMed:20178742}.
Subcellular locationNucleus, nucleoplasm {ECO:0000250}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q92541
Gene Ontology
(Biological Process)
Complete annatation
blastocyst growth [GO:0001832];
endodermal cell fate commitment [GO:0001711];
histone H3-K4 trimethylation [GO:0080182];
negative regulation of transcription from RNA polymerase II promoter [GO:0000122];
positive regulation of histone H3-K4 methylation [GO:0051571];
positive regulation of transcription elongation from RNA polymerase II promoter [GO:0032968];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
stem cell population maintenance [GO:0019827];
transcription elongation from RNA polymerase II promoter [GO:0006368];
Wnt signaling pathway [GO:0016055]
Gene Ontology
(Molecular Function)
Complete annatation
poly(A RNA binding [GO:0044822];
single-stranded DNA binding [GO:0003697]
Gene Ontology
(Cellular Component)
Complete annatation
Cdc73/Paf1 complex [GO:0016593];
nucleolus [GO:0005730]
Protein-protein interaction116780
Phylogenetic treeQ92541
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. CD30.3936322025757230.229614058547990.339554855811942
AZA vs. DISU0.01296502779686770.9591656934849370.996649735504266
AZA vs. IL7-0.03452473509288990.8575810343098580.999311006273513
AZA vs. SAHA0.05069410099302120.8358408571828930.961440456451378
DISU vs. CD3-0.3931750099923790.2796478964326110.409025071882901
DISU vs. IL7-0.05677349837446330.8217414506549390.961667592689605
DISU vs. SAHA0.03929067259924420.8935907179395720.973945010373438
DMSO vs. AZA0.001352690521585520.9935641958538321
DMSO vs. CD3-0.4042215655141580.206535230503640.306970525605498
DMSO vs. DISU-0.0134123094384010.9562027286716770.993828264951078
DMSO vs. IL7-0.02872964884116170.8731431105011190.972518772476859
DMSO vs. SAHA0.0432142792024350.8549777932478140.962018897148281
HIV vs. Mock in Activation0.1294075832748090.835254806909650.999983755607037
HIV vs. Mock in Latency0.08465423427640250.6082551757704850.999834320637052
IL7 vs. CD3-0.4212764882501750.1904288955718280.31070954134598
SAHA vs. CD3-0.3675734876505520.2988845074835790.41224506020296
SAHA vs. IL70.08198638346216820.7375263112399950.880731332934459
(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 -0.201094 0.145615
(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
1.019 1.003 0.905 0.835 1.055
(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
2BZE NMR - A=353-484.
2DB9 NMR - A=347-482.
3U1U X-ray 1.8Å A/B=347-482.
4L1P X-ray 2.1Å A/B=353-484.
4L1U X-ray 2.4Å A/B/C/D/E/F=353-484.

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

HIV Partner Interaction Type PubMed
HIV-1 virus replication inhibited by expression of human gene 22082156

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found