Protein Information (annotations from UniProt)
| Database ID | HIV0002568 |
| UniProt ID | Q92541 |
| Primary gene name(s) | RTF1 |
| Synonym gene name(s) | KIAA0252 |
| Protein name | RNA polymerase-associated protein RTF1 homolog |
| Protein function | Component 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 location | Nucleus, nucleoplasm {ECO:0000250}. |
| ECO code | Click here for more information. |
| Amino acid sequence FASTA format: Q92541 |
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| 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 interaction | 116780 |
| Phylogenetic tree | Q92541 |
| 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 | 0.393632202575723 | 0.22961405854799 | 0.339554855811942 |
| AZA vs. DISU | 0.0129650277968677 | 0.959165693484937 | 0.996649735504266 |
| AZA vs. IL7 | -0.0345247350928899 | 0.857581034309858 | 0.999311006273513 |
| AZA vs. SAHA | 0.0506941009930212 | 0.835840857182893 | 0.961440456451378 |
| DISU vs. CD3 | -0.393175009992379 | 0.279647896432611 | 0.409025071882901 |
| DISU vs. IL7 | -0.0567734983744633 | 0.821741450654939 | 0.961667592689605 |
| DISU vs. SAHA | 0.0392906725992442 | 0.893590717939572 | 0.973945010373438 |
| DMSO vs. AZA | 0.00135269052158552 | 0.993564195853832 | 1 |
| DMSO vs. CD3 | -0.404221565514158 | 0.20653523050364 | 0.306970525605498 |
| DMSO vs. DISU | -0.013412309438401 | 0.956202728671677 | 0.993828264951078 |
| DMSO vs. IL7 | -0.0287296488411617 | 0.873143110501119 | 0.972518772476859 |
| DMSO vs. SAHA | 0.043214279202435 | 0.854977793247814 | 0.962018897148281 |
| HIV vs. Mock in Activation | 0.129407583274809 | 0.83525480690965 | 0.999983755607037 |
| HIV vs. Mock in Latency | 0.0846542342764025 | 0.608255175770485 | 0.999834320637052 |
| IL7 vs. CD3 | -0.421276488250175 | 0.190428895571828 | 0.31070954134598 |
| SAHA vs. CD3 | -0.367573487650552 | 0.298884507483579 | 0.41224506020296 |
| SAHA vs. IL7 | 0.0819863834621682 | 0.737526311239995 | 0.880731332934459 |
| (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 |
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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 | -0.201094 | 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) |
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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 | ||
| 1.019 | 1.003 | 0.905 | 0.835 | 1.055 | ||
| (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
Metabolic/Signalling Pathway (annotations from KEGG database) top
| Pathway Accession Number | Description | not found |
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