UPF2

General Information

Full gene name:UPF2 regulator of nonsense transcripts homolog (yeast) Entrez Gene ID:26019 Location:10p14-p13 Synonyms:smg-3, RENT2, HUPF2 Type:protein-coding

User SNPs

SNPs given by the user that are near or inside this gene:

SNP	Distance (bp)	Direction
rs12779790	242987	upstream

NCBI Summary

This gene encodes a protein that is part of a post-splicing multiprotein 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 the perinuclear area. It interacts with translation release factors and the proteins that are functional homologs of yeast Upf1p and Upf3p. Two splice variants have been found for this gene; both variants encode the same protein. [provided by RefSeq, Jul 2008]

OMIM

OMIM ID:`OMIM ID 605529 `_

NCBI Phenotypes

• A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
• NHGRI GWA Catalog

Gene Ontology

• cytosol
• RNA binding
• liver development
• DNA binding
• organ regeneration
• cytoplasm
• nucleus
• RNA metabolic process
• protein binding
• exon-exon junction complex
• perinuclear region of cytoplasm
• mRNA export from nucleus
• gene expression
• mRNA metabolic process
• nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

KEGG Pathways

• mRNA surveillance pathway
• RNA transport

GeneRIFs

• UPF2-silenced HeLa cells were impaired in their ability to recognize ectopically expressed aberrant premature termination codon transcripts [PMID 16449641]
• UPF2 and UPF3b cooperatively stimulate both ATPase and RNA helicase activities of UPF1. [PMID 18066079]
• Two-hybrid [PMID 11073994]
• During nonsense-mediated mRNA decay, CBP80 interacts with Upf1 and promotes the interaction of Upf1 with Upf2 but not with Stau1. [PMID 16186820]
• Affinity Capture-Western [PMID 14527413]
• Affinity Capture-Western [PMID 14527413]
• Affinity Capture-Western [PMID 14527413]
• Affinity Capture-Western [PMID 14527413]
• Affinity Capture-Western [PMID 14527413]
• Affinity Capture-Western [PMID 14527413]
• Affinity Capture-Western [PMID 14527413]
• Affinity Capture-Western [PMID 14527413]
• The complex between the interacting domains of human UPF2 and UPF3b at a 1.95 A resolution. [PMID 15004547]
• Affinity Capture-MS [PMID 21139048]
• Observational study and genome-wide association study of gene-disease association. (HuGE Navigator) [PMID 18987618]
• Affinity Capture-Western; Two-hybrid [PMID 15231747]
• Two-hybrid [PMID 15231747]
• Two-hybrid [PMID 15231747]
• Two-hybrid [PMID 15231747]
• Two-hybrid [PMID 15231747]
• Two-hybrid [PMID 15231747]
• Data show that upon binding to Upf2, the regulatory CH domain of Upf1 undergoes a large conformational change, causing the catalytic helicase domain to bind RNA less extensively and triggering its helicase activity. [PMID 21419344]
• Affinity Capture-MS; Affinity Capture-Western [PMID 16488880]
• Affinity Capture-Western [PMID 16488880]
• The authors propose that the bipartite mode of UPF2 binding to UPF1 brings the ribosome and the exon junction complex in close proximity by forming a tight complex after an initial weak encounter with either element. [PMID 19556969]
• Observational study of gene-disease association. (HuGE Navigator) [PMID 16385451]
• The Upf complex communicates with the exon-junction complex and triggers nonsense-mediated decay in the cytoplasm. [PMID 17803942]
• Upf1 interacts with Upf2. [PMID 15680326]
• Affinity Capture-Western [PMID 11544179]

PubMed Articles

Recent articles:

• Tao S et al. “A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.” Carcinogenesis. 2012 Mar;33(3):598-603. PMID 22219177
• Chakrabarti S et al. “Molecular mechanisms for the RNA-dependent ATPase activity of Upf1 and its regulation by Upf2.” Mol Cell. 2011 Mar 18;41(6):693-703. PMID 21419344
• Danielsen JM et al. “Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.” Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. PMID 21139048
• Clerici M et al. “Unusual bipartite mode of interaction between the nonsense-mediated decay factors, UPF1 and UPF2.” EMBO J. 2009 Aug 5;28(15):2293-306. PMID 19556969
• Cronin S et al. “Screening for replication of genome-wide SNP associations in sporadic ALS.” Eur J Hum Genet. 2009 Feb;17(2):213-8. PMID 18987618
• Woeller CF et al. “NMD resulting from encephalomyocarditis virus IRES-directed translation initiation seems to be restricted to CBP80/20-bound mRNA.” EMBO Rep. 2008 May;9(5):446-51. PMID 18369367
• Chamieh H et al. “NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity.” Nat Struct Mol Biol. 2008 Jan;15(1):85-93. PMID 18066079
• Singh G et al. “Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm.” Mol Cell. 2007 Sep 7;27(5):780-92. PMID 17803942
• Morris C et al. “Human INT6/eIF3e is required for nonsense-mediated mRNA decay.” EMBO Rep. 2007 Jun;8(6):596-602. PMID 17468741
• You KT et al. “Selective translational repression of truncated proteins from frameshift mutation-derived mRNAs in tumors.” PLoS Biol. 2007 May;5(5):e109. PMID 17456004

Top Pubmed articles linked to gene UPF2 matching any search term:

• Tao S et al. “A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.” Carcinogenesis. 2012 Mar;33(3):598-603. PMID 22219177