Upf1

Wednesday, 23 April 2025

UPF1 regulator of nonsense transcripts homolog (yeast)

PDB rendering based on 2gjk.

Available structures

Ortholog search: PDBe, RCSB

List of PDB id codes
2GJK, 2GK6, 2GK7, 2IYK, 2WJV, 2WJY, 2XZO, 2XZP

Identifiers

Symbols

UPF1; HUPF1; NORF1; RENT1; pNORF1; smg-2

External IDs

OMIM: 601430 MGI: 107995 HomoloGene: 2185 GeneCards: UPF1 Gene

Gene Ontology
Molecular function	• nucleotide binding • DNA binding • chromatin binding • RNA binding • ATP-dependent RNA helicase activity • helicase activity • protein binding • ATP binding • zinc ion binding • hydrolase activity • metal ion binding
Cellular component	• chromatin • cytoplasmic mRNA processing body • cytoplasm • cytosol • exon-exon junction complex
Biological process	• nuclear-transcribed mRNA catabolic process, nonsense-mediated decay • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay • DNA replication • DNA repair • mRNA export from nucleus • regulation of translational termination • regulation of translational termination • cell cycle • gene expression • RNA metabolic process • mRNA metabolic process • histone mRNA catabolic process
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 19:
18.94 – 18.98 Mb

Chr 8:
72.86 – 72.88 Mb

PubMed search

[1]

[2]

Regulator of nonsense transcripts 1 is a protein that in humans is encoded by the UPF1 gene.^[1]^[2]

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 only in the cytoplasm. When translation ends, it interacts with the protein that is a functional homolog of yeast Upf2p to trigger mRNA decapping. Use of multiple polyadenylation sites has been noted for this gene.^[3]

Interactions [link]

UPF1 has been shown to interact with UPF2,^[4]^[5]^[6]^[7]^[8] SMG1,^[7] DCP2,^[4]^[9] DCP1A,^[9] UPF3A^[5]^[7]^[8] and UPF3B.^[4]^[5]^[8]

References [link]

^ 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. DOI:10.1073/pnas.93.20.10928. PMC 38260. PMID 8855285. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=38260.
^ 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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=146496.
^ "Entrez Gene: UPF1 UPF1 regulator of nonsense transcripts homolog (yeast)". https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5976.
^ ^a ^b ^c Lejeune, Fabrice; Li Xiaojie, Maquat Lynne E (September 2003). "Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities". Mol. Cell (United States) 12 (3): 675–87. DOI:10.1016/S1097-2765(03)00349-6. ISSN 1097-2765. PMID 14527413.
^ ^a ^b ^c Schell, Thomas; Köcher Thomas, Wilm Matthias, Seraphin Bertrand, Kulozik Andreas E, Hentze Matthias W (August 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. (England) 373 (Pt 3): 775–83. DOI:10.1042/BJ20021920. ISSN 0264-6021. PMC 1223536. PMID 12723973. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1223536.
^ Mendell, J T; Medghalchi S M, Lake R G, Noensie E N, Dietz H C (Dec. 2000). "Novel Upf2p Orthologues Suggest a Functional Link between Translation Initiation and Nonsense Surveillance Complexes". Mol. Cell. Biol. (UNITED STATES) 20 (23): 8944–57. DOI:10.1128/MCB.20.23.8944-8957.2000. ISSN 0270-7306. PMC 86549. PMID 11073994. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=86549.
^ ^a ^b ^c Yamashita, A; Ohnishi T, Kashima I, Taya Y, Ohno S (September 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. (United States) 15 (17): 2215–28. DOI:10.1101/gad.913001. ISSN 0890-9369. PMC 312771. PMID 11544179. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=312771.
^ ^a ^b ^c Lykke-Andersen, J; Shu M D, Steitz J A (Dec. 2000). "Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon". Cell (United States) 103 (7): 1121–31. DOI:10.1016/S0092-8674(00)00214-2. ISSN 0092-8674. PMID 11163187.
^ ^a ^b Lykke-Andersen, Jens (Dec. 2002). "Identification of a Human Decapping Complex Associated with hUpf Proteins in Nonsense-Mediated Decay". Mol. Cell. Biol. (United States) 22 (23): 8114–21. DOI:10.1128/MCB.22.23.8114-8121.2002. ISSN 0270-7306. PMC 134073. PMID 12417715. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=134073.

Further reading [link]

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. 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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=316864.
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. PMC 84455. PMID 10454541. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=84455.
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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1369996.
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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=86549.
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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=88795.
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.
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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=312771.
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. DOI:10.1126/science.1062786. PMID 11546874.
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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=115286.
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.
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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=134073.
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. DOI:10.1073/pnas.242603899. PMC 139241. PMID 12477932. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=139241.
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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1370372.
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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1223536.

PDB gallery

2gjk: Structural and functional insights into the human Upf1 helicase core

2gk6: Structural and Functional insights into the human Upf1 helicase core

2gk7: Structural and Functional insights into the human Upf1 helicase core

2iyk: CRYSTAL STRUCTURE OF THE UPF2-INTERACTING DOMAIN OF NONSENSE MEDIATED MRNA DECAY FACTOR UPF1

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Interactions [link]

References [link]

Further reading [link]

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