UPF1

UPF1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2GJK, 2GK6, 2GK7, 2IYK, 2WJV, 2WJY, 2XZO, 2XZP
Identifiers
Aliases	UPF1 , HNORF1, RENT1, pNORF1, smg-2, RNA helicase and ATPase, UPF1 RNA helicase and ATPase, UTF
External IDs	OMIM: 601430; MGI: 107995; HomoloGene: 2185; GeneCards: UPF1; OMA:UPF1 - orthologs
Gene location (Human) Chr. Chromosome 19 (human) [1] Band 19p13.11 Start 18,831,959 bp [1] End 18,868,230 bp [1]
Gene location (Mouse) Chr. Chromosome 8 (mouse) [2] Band 8 B3.3|8 34.15 cM Start 70,784,175 bp [2] End 70,805,928 bp [2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in right hemisphere of cerebellum mucosa of transverse colon olfactory zone of nasal mucosa granulocyte skin of leg anterior pituitary right uterine tube right testis right lobe of thyroid gland stromal cell of endometrium Top expressed in spermatocyte aortic valve granulocyte lip ascending aorta secondary oocyte ventricular zone yolk sac muscle of thigh neural layer of retina More reference expression data BioGPS More reference expression data
Gene ontology Molecular function nucleotide binding DNA binding telomeric DNA binding zinc ion binding chromatin binding metal ion binding protein binding hydrolase activity ATP binding helicase activity RNA binding Cellular component cytosol P-body exon-exon junction complex supraspliceosomal complex nucleoplasm chromatin cytoplasm nucleus Biological process regulation of translational termination telomere maintenance via semi-conservative replication positive regulation of mRNA catabolic process mRNA export from nucleus DNA replication nuclear-transcribed mRNA catabolic process cellular response to interleukin-1 nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay histone mRNA catabolic process dosage compensation by inactivation of X chromosome cellular response to lipopolysaccharide 3'-UTR-mediated mRNA destabilization DNA repair nuclear-transcribed mRNA catabolic process, nonsense-mediated decay regulation of telomere maintenance cell cycle phase transition viral process Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 5976 19704 Ensembl ENSG00000005007 ENSMUSG00000058301 UniProt Q92900 Q9EPU0 RefSeq (mRNA) NM_002911 NM_001297549 NM_001122829 NM_030680 RefSeq (protein) NP_001284478 NP_002902 NP_001284478.1 NP_001116301 NP_109605 Location (UCSC) Chr 19: 18.83 – 18.87 Mb Chr 8: 70.78 – 70.81 Mb PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Regulator of nonsense transcripts 1 (or Up-frameshift suppressor 1 homolog ^[5] ) is a protein that in humans is encoded by the UPF1 gene. ^{[6] [7]}

Function

This gene encodes a protein that is part of a post-splicing multiprotein complex, the exon junction complex, involved in both mRNA nuclear export and mRNA surveillance. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein is located in both the cytoplasm and nucleus. ^[8] When translation ends, it interacts with the functional homolog of yeast Upf2p to trigger mRNA decapping. Use of multiple polyadenylation sites has been noted for this gene. ^[9]

Interactions

UPF1 interacts with:

• DCP1A, ^[10]
• DCP2, ^{[10] [11]}
• SMG1, ^[12]
• UPF2, ^{[11] [12] [13] [14] [15]}
• UPF3A, ^{[12] [13] [15]} and
• UPF3B. ^{[11] [13] [15]}

References

1. GRCh38: Ensembl release 89: ENSG00000005007 – Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000058301 – Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. "UniProt". www.uniprot.org. Retrieved 2024-09-28.
6. Perlick HA, Medghalchi SM, Spencer FA, Kendzior RJ Jr, Dietz HC (November 1996). "Mammalian orthologues of a yeast regulator of nonsense transcript stability". Proc Natl Acad Sci U S A. 93 (20): 10928–32. Bibcode:1996PNAS...9310928P. doi: 10.1073/pnas.93.20.10928 . PMC   38260 . PMID   8855285.
7. Applequist SE, Selg M, Raman C, Jack HM (March 1997). "Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein". Nucleic Acids Res. 25 (4): 814–21. doi:10.1093/nar/25.4.814. PMC   146496 . PMID   9064659.
8. Singh AK, Choudhury SR, De S, Zhang J, Kissane S, Dwivedi V, et al. (March 2019). Singer RH, Manley JL (eds.). "The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci". eLife. 8: e41444. doi: 10.7554/eLife.41444 . PMC   6447362 . PMID   30907728.
9. "UPF1 UPF1 RNA helicase and ATPase [ Homo sapiens (human) ]".
10. Lykke-Andersen J (2002). "Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay". Mol. Cell. Biol. 22 (23): 8114–21. doi:10.1128/MCB.22.23.8114-8121.2002. PMC   134073 . PMID   12417715.
11. Lejeune F, Li X, Maquat LE (2003). "Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities". Mol. Cell. 12 (3): 675–87. doi: 10.1016/S1097-2765(03)00349-6 . PMID   14527413.
12. Yamashita A, Ohnishi T, Kashima I, Taya Y, Ohno S (2001). "Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay". Genes Dev. 15 (17): 2215–28. doi:10.1101/gad.913001. PMC   312771 . PMID   11544179.
13. Schell T, Köcher T, Wilm M, Seraphin B, Kulozik AE, Hentze MW (2003). "Complexes between the nonsense-mediated mRNA decay pathway factor human upf1 (up-frameshift protein 1) and essential nonsense-mediated mRNA decay factors in HeLa cells". Biochem. J. 373 (Pt 3): 775–83. doi:10.1042/BJ20021920. PMC   1223536 . PMID   12723973.
14. Mendell JT, Medghalchi SM, Lake RG, Noensie EN, Dietz HC (2000). "Novel Upf2p orthologues suggest a functional link between translation initiation and nonsense surveillance complexes". Mol. Cell. Biol. 20 (23): 8944–57. doi:10.1128/MCB.20.23.8944-8957.2000. PMC   86549 . PMID   11073994.
15. Lykke-Andersen J, Shu MD, Steitz JA (2000). "Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon". Cell. 103 (7): 1121–31. doi: 10.1016/S0092-8674(00)00214-2 . PMID   11163187. S2CID   18417600.

Further reading

• Azzalin CM, Lingner J (2006). "The double life of UPF1 in RNA and DNA stability pathways". Cell Cycle. 5 (14): 1496–8. doi: 10.4161/cc.5.14.3093 . PMID   16861888.
• Horikoshi M, Sekimizu K, Natori S (1984). "Analysis of the stimulatory factor of RNA polymerase II in the initiation and elongation complex". J. Biol. Chem. 259 (1): 608–11. doi: 10.1016/S0021-9258(17)43705-7 . PMID   6200476.
• Nagase T, Seki N, Ishikawa K, et al. (1997). "Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain". DNA Res. 3 (5): 321–9, 341–54. doi: 10.1093/dnares/3.5.321 . PMID   9039502.
• Czaplinski K, Ruiz-Echevarria MJ, Paushkin SV, et al. (1998). "The surveillance complex interacts with the translation release factors to enhance termination and degrade aberrant mRNAs". Genes Dev. 12 (11): 1665–77. doi:10.1101/gad.12.11.1665. PMC   316864 . PMID   9620853.
• Page MF, Carr B, Anders KR, et al. (1999). "SMG-2 Is a Phosphorylated Protein Required for mRNA Surveillance in Caenorhabditis elegans and Related to Upf1p of Yeast". Mol. Cell. Biol. 19 (9): 5943–51. doi:10.1128/MCB.19.9.5943. PMC   84455 . PMID   10454541.
• Bhattacharya A, Czaplinski K, Trifillis P, et al. (2000). "Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay". RNA. 6 (9): 1226–35. doi:10.1017/S1355838200000546. PMC   1369996 . PMID   10999600.
• Mendell JT, Medghalchi SM, Lake RG, et al. (2000). "Novel Upf2p Orthologues Suggest a Functional Link between Translation Initiation and Nonsense Surveillance Complexes". Mol. Cell. Biol. 20 (23): 8944–57. doi:10.1128/MCB.20.23.8944-8957.2000. PMC   86549 . PMID   11073994.
• Serin G, Gersappe A, Black JD, et al. (2001). "Identification and Characterization of Human Orthologues to Saccharomyces cerevisiae Upf2 Protein and Upf3 Protein (Caenorhabditis elegans SMG-4)". Mol. Cell. Biol. 21 (1): 209–23. doi:10.1128/MCB.21.1.209-223.2001. PMC   88795 . PMID   11113196.
• Lykke-Andersen J, Shu MD, Steitz JA (2001). "Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon". Cell. 103 (7): 1121–31. doi: 10.1016/S0092-8674(00)00214-2 . PMID   11163187. S2CID   18417600.
• Denning G, Jamieson L, Maquat LE, et al. (2001). "Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein". J. Biol. Chem. 276 (25): 22709–14. doi: 10.1074/jbc.C100144200 . PMID   11331269.
• Yamashita A, Ohnishi T, Kashima I, et al. (2001). "Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay". Genes Dev. 15 (17): 2215–28. doi:10.1101/gad.913001. PMC   312771 . PMID   11544179.
• Lykke-Andersen J, Shu MD, Steitz JA (2001). "Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1". Science. 293 (5536): 1836–9. Bibcode:2001Sci...293.1836L. doi:10.1126/science.1062786. PMID   11546874. S2CID   389385.
• Carastro LM, Tan CK, Selg M, et al. (2002). "Identification of delta helicase as the bovine homolog of HUPF1: demonstration of an interaction with the third subunit of DNA polymerase delta". Nucleic Acids Res. 30 (10): 2232–43. doi:10.1093/nar/30.10.2232. PMC   115286 . PMID   12000843.
• Mendell JT, ap Rhys CM, Dietz HC (2002). "Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts". Science. 298 (5592): 419–22. doi: 10.1126/science.1074428 . PMID   12228722. S2CID   46447414.
• Lykke-Andersen J (2003). "Identification of a Human Decapping Complex Associated with hUpf Proteins in Nonsense-Mediated Decay". Mol. Cell. Biol. 22 (23): 8114–21. doi:10.1128/MCB.22.23.8114-8121.2002. PMC   134073 . PMID   12417715.
• Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. Bibcode:2002PNAS...9916899M. doi: 10.1073/pnas.242603899 . PMC   139241 . PMID   12477932.
• Chiu SY, Serin G, Ohara O, Maquat LE (2003). "Characterization of human Smg5/7a: A protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1". RNA. 9 (1): 77–87. doi:10.1261/rna.2137903. PMC   1370372 . PMID   12554878.
• Schell T, Köcher T, Wilm M, et al. (2003). "Complexes between the nonsense-mediated mRNA decay pathway factor human upf1 (up-frameshift protein 1) and essential nonsense-mediated mRNA decay factors in HeLa cells". Biochem. J. 373 (Pt 3): 775–83. doi:10.1042/BJ20021920. PMC   1223536 . PMID   12723973.