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FLASH GENE
Symbol UPF1 contributors: mct/pgu - updated : 10-01-2015
HGNC name UPF1 regulator of nonsense transcripts homolog (yeast)
HGNC id 9962
Location 19p13.11      Physical location : 18.942.743 - 18.979.038
Synonym name
  • up-frameshift mutation1, S-cerevisiae homolog
  • regulator of nonsense transcripts 1
  • UP Frameshift 1
  • ATP-dependent helicase RENT1
  • yeast Upf1p homolog
  • Synonym symbol(s) KIAA0221, HUPF1, PNORF1, RENT1, NORF1, FLJ43809, FLJ46894
    EC.number 3.6.1.-
    DNA
    TYPE functioning gene
    STRUCTURE 36.29 kb     24 Exon(s)
    MAPPING cloned Y linked N status provisional
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    24 - 5360 - 1118 - 2006 16488880
    EXPRESSION
    Type
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Digestivesalivary gland   highly
    Lymphoid/Immunelymph node   highly
    Nervousnerve   moderately
    Reproductivefemale systemuteruscervix moderately
     female systemplacenta  moderately
     male systemtestis  highly
    Respiratoryrespiratory tractlarynx  moderately
    Skin/Tegumentskin   highly
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • an atypical C2H2-type zinc-finger domain
  • a C4-type zinc-finger domain
  • regulatory CH domain of Upf1 undergoing a large conformational change
  • two ST-Q motif, directly interacting with the helicase domain to impede ATP hydrolysis and RNA unwinding
  • C-terminal domain, conserved in higher eukaryotes and containing several essential phosphorylation sites, also inhibits the flanking helicase domain
  • HOMOLOGY
    interspecies homolog to murine Upf1 (98.8 pc)
    Homologene
    FAMILY
  • DNA2/NAM7 helicase family
  • CATEGORY enzyme , regulatory , RNA associated
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,cytoplasm
    intracellular,nucleus,chromatin/chromosome
    text
  • mainly localizes to the cytoplasm and, via mechanisms that are linked to translation termination but not yet well understood, stimulates rapid destruction of mRNAs carrying a PTC (premature translation termination codon)
  • basic FUNCTION
  • acting as a regulator of nonsense transcript, detecting and degrading transcripts with a premature signal of termination of translation
  • being essential for embryonic viability
  • acting as an ATP-dependent RNA helicase
  • inhibiting translation termination
  • UPF1 and UPF2 assemble on polysomes for recognition of aberrant mRNAs containing premature termination codons
  • may participate in RNA silencing by facilitating the binding of the RNA-induced silencing complex to the target and by accelerating the decay of the mRNA
  • UPF1 ATPase-dependent messenger ribonucleoprotein disassembly is required for completion of nonsense- mediated mRNA decay
  • crucial factor in nonsense-mediated mRNA decay, the eukaryotic surveillance pathway that degrades mRNAs containing premature stop codons
  • orchestrates crucial aspects of telomere biology, including telomere replication and telomere length homeostasis
  • key player in nonsense-mediated mRNA decay
  • sustains the proper replication of telomeres, the protective structures located at the ends of linear eukaryotic chromosomes
  • evolutionarily conserved protein with RNA/DNA-dependent ATPase and RNA helicase activity
  • contributes to DNA replication, DNA repair, telomere metabolism, and stabilization of HIV-1 genomic RNA
  • implicated in nuclear functions
  • multifaceted eukaryotic enzyme involved in DNA replication, telomere metabolism and several mRNA degradation pathways
  • UPF3B and UPF1 are down-regulated during differentiation of neural stem cells into neurons
  • ATP hydrolysis by UPF1 modulates a functional interaction between the NMD machinery and terminating ribosomes necessary for targeting substrates to accelerated degradation
  • CELLULAR PROCESS nucleotide, replication
    nucleotide, repair
    protein, translation regulation
    PHYSIOLOGICAL PROCESS
    text
  • mRNA export from nucleus
  • regulation of translational termination
  • PATHWAY
    metabolism
    signaling
    a component
  • component of the mRNA decay complex (DCP2, LSM1, LSM3, LSM4, EXOSC2, EXOSC4, EXOSC10, PARN, XRN1, CCRN4L, RENT1, UPF2, UPF3B)
  • part of a post-splicing multiprotein complex
  • INTERACTION
    DNA
    RNA
    small molecule metal binding, nucleotide,
  • ATP
  • Zn2+
  • protein
  • interacting with DCP2
  • interacting with SMG6
  • binding to ERF1 and to the GTPase domain of ERF3 both in its GTP- and GDP-bound states
  • in the UPF trimeric complex, UPF2 and UPF3B cooperatively stimulate both ATPase and RNA helicase activities of UPF1 (pMID: 18066079)
  • association with the cap-binding protein, NCBP1, promotes nonsense-mediated mRNA decay at two distinct steps
  • 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
  • association with telomeres is stimulated by the phosphoinositide 3-kinase (PI3K)-related protein kinase ataxia telangiectasia mutated and Rad3-related (ATR) and by telomere elongation
  • physically interacts with the telomeric factor TPP1 and with telomerase
  • recruitment of STAU2 alone or in combination with UPF1 differentially affects the fate of mRNAs
  • also interacts with proteins associated with nuclear RNA degradation and transcription termination
  • MOV10 functions in UPF1-mediated mRNA degradation as an RNA clearance factor to resolve structures and displace proteins from 3prime UTRs
  • SMG1C (a complex containing SMG1, SMG8, and SMG9) contributes to regulate NMD by recruiting UPF1 and UPF2 to distinct sites in the vicinity of the kinase domain
  • DHX34 is recruited to the SURF complex via its preferential interaction with hypophosphorylated UPF1
  • ability of UPF1 to impinge on premature termination, moreover, requires ATP-binding, RNA-binding and NMD cofactors UPF2 and UPF3
  • UPF1 and ribosomes are new interaction partners of UPF3B
  • cell & other
    REGULATION
    Other phosphorylation by SMG1 required for formation of mRNA surveillance complexes
    phosphorylated upon DNA damage, probably by ATM or ATR
    ASSOCIATED DISORDERS
    ANIMAL & CELL MODELS