Alternative titles; symbols
HGNC Approved Gene Symbol: UPF1
Cytogenetic location: 19p13.11 Genomic coordinates (GRCh38): 19:18,831,959-18,868,230 (from NCBI)
UPF1 is a helicase that shows RNA-dependent ATPase and 5-prime-to-3-prime RNA helicase activities. The ATPase activity of UPF1 is critical to the nonsense-mediated RNA decay (NMD) pathway, which targets mRNAs with premature termination codons for rapid degradation (summary by Franks et al., 2010).
Perlick et al. (1996) noted that at least 3 transacting factors (Upf1-3) are required for NMD in yeast. They identified a human cDNA encoding a protein with strong homology to Upf1 that they termed RENT1. Although divergence exists at the extreme N and C termini of the human and yeast polypeptides, the large central region of the protein shows 58% residue identity and 80% conservation. Perlick et al. (1996) stated that RENT1 is the first identified mammalian protein that contains all of the putative functional elements found in Upf1, including zinc finger-like nucleotide-binding domains and all the motifs common to members of helicase superfamily I. By cloning of the mouse gene and subsequent alignment of the sequences for all related helicases, Perlick et al. (1996) demonstrated that RENT1, Upf1, Mov10, and Sen1 define a distinct subset within the superfamily. As expected for an essential component of the apparently ubiquitous NMD pathway, RENT1 was detected in all tissues tested.
Independently, Applequist et al. (1997) isolated cDNAs encoding RENT1, which they named HUPF1 (human Upf1 protein). They stated that HUPF1 encodes a predicted 1,118-amino acid protein. Western blot analysis of human cell extracts showed that HUPF1 migrated as a 130-kD protein. Using immunofluorescence, Applequist et al. (1997) found that human and mouse HUPF1, like yeast Upf1, localized in the cytoplasm but not in the nucleus. Northern blot analysis detected a predominant 5.5-kb HUPF1 mRNA and a minor 3.7-kb HUPF1 mRNA in various human cell lines.
Perlick et al. (1996) found that expression of a chimeric protein containing the central region of human RENT1 flanked by the extreme N and C termini of yeast Upf1 complemented the Upf1-deficient growth phenotype in yeast. These data demonstrated that RENT1 is a mammalian ortholog of Upf1.
Sun et al. (1998) provided evidence for a factor that functions to eliminate the production of nonsense-containing RNAs in mammalian cells. They identified the factor, variously referred to as RENT1 and HUPF1, by isolating cDNA for a human homolog of S. cerevisiae Upf1p, which is a group I RNA helicase that functions in the nonsense-mediated decay of mRNA in yeast. Using monkey COS cells and human HeLa cells, Sun et al. (1998) demonstrated that expression of human Upf1 protein harboring an arginine-to-cysteine mutation at residue 844 within the RNA helicase domain acts in a dominant-negative fashion to abrogate the decay of nonsense-containing mRNA that takes place in association with nuclei or in the cytoplasm. These findings provided evidence that nonsense-mediated mRNA decay is related mechanistically in yeast and in mammalian cells, regardless of the cellular site of decay.
Mendell et al. (2002) assessed the role of factors essential for NMD in nonsense-mediated altered splicing (NAS) with the use of RNA interference in mammalian cells. Inhibition of RENT1 expression abrogated both NMD and NAS of nonsense T-cell receptor beta (TCRB; see 186930) transcripts. In contrast, inhibition of RENT2 (UPF2; 605529) expression did not disrupt NAS despite achieving comparable stabilization of nonsense transcripts. Mendell et al. (2002) also demonstrated that NAS and NMD are genetically separable functions of RENT1. Mendell et al. (2002) demonstrated that RENT1 enters the nucleus, where it may directly influence early events in mRNA biogenesis. Mendell et al. (2002) concluded that their results provide compelling evidence that NAS relies on a component of the nonsense surveillance machinery but is not an indirect consequence of NMD.
Using immunoprecipitation and immunodepletion experiments, Ohnishi et al. (2003) showed that SMG5 (610962) and SMG7 (610964) associated with a hyperphosphorylated form of UPF1, and that SMG5 was involved in UPF1 dephosphorylation by the protein phosphatase-2A (PP2A; see 176915) complex. SMG5 mutants that interfered with UPF1 dephosphorylation also inhibited nonsense-mediated mRNA decay in a dominant-negative manner.
Amrani et al. (2004) used a primer extension inhibition (toeprinting) assay to delineate ribosome positioning and found that premature translation termination in yeast extracts is indeed aberrant. Ribosomes encountering premature UAA or UGA codons in the Can1 mRNA failed to release and, instead, migrated to upstream AUGs. This anomaly depended upon prior nonsense codon recognition and was eliminated in extracts derived from cells lacking the principal NMD factor Upf1p, or by flanking the nonsense codon with a normal 3-prime untranslated region (UTR). Tethered poly(A)-binding protein (Pab1p), used as a mimic of a normal 3-prime UTR, recruited the termination factor Sup35p (eRF3) and stabilized nonsense-containing mRNAs. Amrani et al. (2004) concluded that efficient termination and mRNA stability are dependent on a properly configured 3-prime UTR.
Staufen-1 (STAU1; 601716) is an RNA-binding protein that is thought to function in mRNA transport and translational control. Kim et al. (2005) described an mRNA decay mechanism involving STAU1, UPF1, and a termination codon. Unlike nonsense-mediated decay, this mechanism did not involve pre-mRNA splicing and occurred when UPF2 or UPF3X (UPF3B; 300298) was downregulated. STAU1 bound directly to UPF1 and elicited mRNA decay when tethered downstream of a termination codon. STAU1 also interacted with the 3-prime UTR of ADP-ribosylation factor-1 (ARF1; 103180) mRNA. Accordingly, downregulation of either STAU1 or UPF1 increased ARF1 mRNA stability. These findings suggested that ARF1 mRNA is a natural target for STAU1-mediated decay, and data indicated that other mRNAs are also natural targets.
In crosslinking and coimmunoprecipitation experiments on HeLa cell nuclear extracts, Agranat et al. (2008) showed that ADAR1 (146920) associated with the RNA surveillance protein HUPF1 in the supraspliceosome, a 21-megadalton nuclear ribonucleoprotein complex. The interaction did not depend on RNA. Knockdown of ADAR1 with small interfering RNA upregulated the expression of 4 of 6 genes that undergo both A-to-I editing by ADARs and degradation via HUPF1.
Cellular mRNAs exist as messenger ribonucleoprotein (mRNP) complexes containing the mRNA and associated proteins. Franks et al. (2010) found that small interfering RNA-mediated knockdown of UPF1 in HeLa cells or expression of an ATPase-deficient UPF1 mutant caused accumulation of an NMD mRNP in cytoplasmic processing bodies. In the absence of UPF1 ATPase activity, the NMD factors SMG5, SMG6 (610963), and SMG7 colocalized with a partially degraded 3-prime mRNA intermediate in cytoplasmic processing bodies. ATPase-deficient UPF1 copurified with multiple NMD factors, including XRN1 (607994) and PABPC1 (604679), in addition to SMG5, SMG6, and SMG7, and with exon junction complex components (see 608546). Franks et al. (2010) concluded that UPF1 ATPase activity is required for disassembly of mRNP complexes, and that disassembly of these complexes is required for degradation of mRNA by XRN1.
Perlick et al. (1996) mapped the mouse Rent1 gene to mouse chromosome 8 by analysis of the Jackson Laboratory BSS backcross DNA panel. The region of mouse chromosome 8 was known to have homology of synteny to 19p13.2-p13.11; the human probe detected human chromosome 19-specific restriction fragments within the NIGMS human/rodent somatic cell hybrid panel. Perlick et al. (1996) noted that although tumorigenic or accelerated aging phenotypes might be predicted to result from the somatic accumulation of nonsense or frameshift mutations on an NMD-deficient background, no apparently relevant phenotypes have been linked to the map positions for the murine or human genes on syntenic regions of chromosomes 8 and 19p13.2-p13.11, respectively.
Somatic Mutation in Pancreatic Adenosquamous Carcinoma
Liu et al. (2014) identified mutations in the UPF1 gene in pancreatic adenosquamous carcinoma (ASC) tumors (see 260350) from 18 of 23 patients. Liu et al. (2014) also tested 3 other NMD genes--UPF2 (605529), UPF3A (605530), and UPF3B (300298)--but did not detect mutations. The UPF1 mutations were somatic in origin, as they were not present in matched normal pancreatic tissues from the 18 patients. UPF1 mutations were also not detectable in 29 non-ASC pancreatic tumors and in 21 lung squamous cell carcinomas that were tested. Liu et al. (2014) concluded that UPF1 mutations are a unique signature of most pancreatic adenosquamous carcinomas.
Medghalchi et al. (2001) explored the consequences of loss of NMD function in vertebrates through targeted disruption of the Rent1 gene, which encodes a mammalian ortholog of Upf1p, in murine embryonic stem cells. Mice heterozygous for the targeted allele showed no apparent phenotypic abnormalities but homozygosity was never observed, demonstrating that Rent1 is essential for embryonic viability. Homozygous targeted embryos showed complete loss of NMD and were viable in the preimplantation period, but resorbed shortly after implantation. Furthermore, Rent1 -/- blastocysts isolated at 3.5 days postcoitum underwent apoptosis in culture following a brief phase of cellular expansion. The authors hypothesized that NMD is essential for mammalian cellular viability and supports a critical role for the pathway in the regulated expression of selected physiologic transcripts.
Agranat, L., Raitskin, O., Sperling, J., Sperling, R. The editing enzyme ADAR1 and the mRNA surveillance protein hUpf1 interact in the cell nucleus. Proc. Nat. Acad. Sci. 105: 5028-5033, 2008. [PubMed: 18362360] [Full Text: https://doi.org/10.1073/pnas.0710576105]
Amrani, N., Ganesan, R., Kervestin, S., Mangus, D. A., Ghosh, S., Jacobson, A. A faux 3-prime-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay. Nature 432: 112-118, 2004. [PubMed: 15525991] [Full Text: https://doi.org/10.1038/nature03060]
Applequist, S. E., Selg, M., Raman, C., Jack, H.-M. Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein. Nucleic Acids Res. 25: 814-821, 1997. [PubMed: 9064659] [Full Text: https://doi.org/10.1093/nar/25.4.814]
Franks, T. M., Singh, G., Lykke-Andersen, J. Upf1 ATPase-dependent mRNP disassembly is required for completion of nonsense-mediated mRNA decay. Cell 143: 938-950, 2010. [PubMed: 21145460] [Full Text: https://doi.org/10.1016/j.cell.2010.11.043]
Kim, Y. K., Furic, L., DesGroseillers, L., Maquat, L. E. Mammalian Staufen1 recruits Upf1 to specific mRNA 3-prime UTRs so as to elicit mRNA decay. Cell 120: 195-208, 2005. [PubMed: 15680326] [Full Text: https://doi.org/10.1016/j.cell.2004.11.050]
Liu, C., Karam, R., Zhou, Y., Su, F., Ji, Y., Li, G., Xu, G., Lu, L., Wang, C., Song, M., Zhu, J., Wang, Y., Zhao, Y., Foo, W. C., Zuo, M., Valasek, M. A., Javle, M., Wilkinson, M. F., Lu, Y. The UPF1 RNA surveillance gene is commonly mutated in pancreatic adenosquamous carcinoma. Nature Med. 20: 596-598, 2014. [PubMed: 24859531] [Full Text: https://doi.org/10.1038/nm.3548]
Medghalchi, S. M., Frischmeyer, P. A., Mendell, J. T., Kelly, A. G., Lawler, A. M., Dietz, H. C. Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. Hum. Molec. Genet. 10: 99-105, 2001. [PubMed: 11152657] [Full Text: https://doi.org/10.1093/hmg/10.2.99]
Mendell, J. T., ap Rhys, C. M. J., Dietz, H. C. Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts. Science 298: 419-371, 2002. [PubMed: 12228722] [Full Text: https://doi.org/10.1126/science.1074428]
Ohnishi, T., Yamashita, A., Kashima, I., Schell, T., Anders, K. R., Grimson, A., Hachiya, T., Hentze, M. W., Anderson, P., Ohno, S. Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. Molec. Cell 12: 1187-1200, 2003. [PubMed: 14636577] [Full Text: https://doi.org/10.1016/s1097-2765(03)00443-x]
Perlick, H. A., Medghalchi, S. M., Spencer, F. A., Dietz, H. C. Cloning and characterization of a human regulator of nonsense transcript stability. (Abstract) Am. J. Hum. Genet. 59 (suppl.): A32 only, 1996.
Perlick, H. A., Medghalchi, S. M., Spencer, F. A., Kendzior, R. J., Jr., Dietz, H. C. Mammalian orthologues of a yeast regulator of nonsense transcript stability. Proc. Nat. Acad. Sci. 93: 10928-10932, 1996. [PubMed: 8855285] [Full Text: https://doi.org/10.1073/pnas.93.20.10928]
Sun, X., Perlick, H. A., Dietz, H. C., Maquat, L. E. A mutated human homologue to yeast Upf1 protein has a dominant-negative effect on the decay of nonsense-containing mRNAs in mammalian cells. Proc. Nat. Acad. Sci. 95: 10009-10014, 1998. [PubMed: 9707591] [Full Text: https://doi.org/10.1073/pnas.95.17.10009]