Addington,, A. M., Gauthier,, J., Piton,, A., Hamdan,, F. F., Raymond,, A., Gogtay,, N., … Rouleau, G. A. (2011). A novel frameshift mutation in UPF3B identified in brothers affected with childhood onset schizophrenia and autism spectrum disorders. Molecular Psychiatry, 16(3), 238–239.
Alkalaeva,, E. Z., Pisarev,, A. V., Frolova,, L. Y., Kisselev,, L. L., & Pestova,, T. V. (2006). In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3. Cell, 125(6), 1125–1136.
Amrani,, N., Ganesan,, R., Kervestin,, S., Mangus,, D. A., Ghosh,, S., & Jacobson,, A. (2004). A faux 3’‐UTR promotes aberrant termination and triggers nonsense‐mediated mRNA decay. Nature, 432(7013), 112–118.
Anastasaki,, C., Longman,, D., Amy,, C., Elizabeth Patton,, E., & Cáceres,, J. F. (2011). Dhx34 and Nbas function in the NMD pathway and are required for embryonic development in Zebrafish. Nucleic Acids Research, 39(9), 3686–3694.
Anders,, K. R., Grimson,, A., & Anderson,, P. (2003). SMG‐5, required for C. elegans nonsense‐mediated mRNA decay, associates with SMG‐2 and protein phosphatase 2A. The EMBO Journal, 22(3), 641–650.
Andersen,, C. B. F., Ballut,, L., Johansen,, J. S., Chamieh,, H., Nielsen,, K. H., Oliveira,, C. L. P., … Andersen,, G. R. (2006). Structure of the exon junction core complex with a trapped DEAD‐box ATPase bound to RNA. Science, 313(5795), 1968–1972.
Aznarez,, I., Nomakuchi,, T. T., Tetenbaum‐Novatt,, J., Rahman,, M. A., Fregoso,, O., Rees,, H., & Krainer,, A. R. (2018). Mechanism of nonsense‐mediated mRNA decay stimulation by splicing factor SRSF1. Cell Reports, 23(7), 2186–2198.
Baird,, T. D., Cheng,, K. C.‐C., Chen,, Y.‐C., Buehler,, E., Martin,, S. E., Inglese,, J., & Hogg,, J. R. (2018). ICE1 promotes the link between splicing and nonsense‐mediated mRNA decay. eLife, 7, e33178. https://doi.org/10.7554/eLife.33178
Baker,, S. L., & Hogg,, J. R. (2017). A system for coordinated analysis of translational readthrough and nonsense‐mediated mRNA decay. PloS One, 12(3), e0173980.
Balagopal,, V., & Beemon,, K. L. (2017). Rous sarcoma virus RNA stability element inhibits deadenylation of mRNAs with long 3’UTRs. Viruses, 9(8), E204. https://doi.org/10.3390/v9080204
Balistreri,, G., Horvath,, P., Schweingruber,, C., Zünd,, D., McInerney,, G., Merits,, A., … Helenius,, A. (2014). The host nonsense‐mediated mRNA decay pathway restricts mammalian RNA virus replication. Cell Host %26 Microbe, 16(3), 403–411.
Ballut,, L., Marchadier,, B., Baguet,, A., Tomasetto,, C., Séraphin,, B., & Le Hir,, H. (2005). The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity. Nature Structural %26 Molecular Biology, 12(10), 861–869.
Behm‐Ansmant,, I., Gatfield,, D., Rehwinkel,, J., Hilgers,, V., & Izaurralde,, E. (2007). A conserved role for cytoplasmic poly(A)‐binding protein 1 (PABPC1) in nonsense‐mediated mRNA decay. The EMBO Journal, 26(6), 1591–1601.
Behm‐Ansmant,, I., & Izaurralde,, E. (2006). Quality control of gene expression: A stepwise assembly pathway for the surveillance complex that triggers nonsense‐mediated mRNA decay. Genes %26 Development, 20(4), 391–398.
Bejerano,, G., Pheasant,, M., Makunin,, I., Stuart,, S., James Kent,, W., Mattick,, J. S., & Haussler,, D. (2004). Ultraconserved elements in the human genome. Science, 304(5675), 1321–1325.
Belew,, A. T., Advani,, V. M., & Dinman,, J. D. (2011). Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast. Nucleic Acids Research, 39(7), 2799–2808.
Belew,, A. T., Meskauskas,, A., Musalgaonkar,, S., Advani,, V. M., Sulima,, S. O., Kasprzak,, W. K., … Dinman,, J. D. (2014). Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway. Nature, 512(7514), 265–269.
Bicknell,, A. A., Cenik,, C., Chua,, H. N., Roth,, F. P., & Moore,, M. J. (2012). Introns in UTRs: Why we should stop ignoring them. BioEssays, 34(12), 1025–1034.
Blatter,, M., Dunin‐Horkawicz,, S., Grishina,, I., Maris,, C., Thore,, S., Maier,, T., … Allain,, F. H.‐T. (2015). The signature of the five‐stranded vRRM Fold defined by functional, structural and computational analysis of the hnRNP L protein. Journal of Molecular Biology, 427(19), 3001–3022.
Boehm,, V., Gerbracht,, J. V., Marx,, M.‐C., & Gehring,, N. H. (2016). Interrogating the degradation pathways of unstable mRNAs with XRN1‐resistant sequences. Nature Communications, 7, 13691.
Boehm,, V., Haberman,, N., Ottens,, F., Ule,, J., & Gehring,, N. H. (2014). 3’ UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons. Cell Reports, 9(2), 555–568.
Buchwald,, G., Ebert,, J., Basquin,, C., Sauliere,, J., Jayachandran,, U., Bono,, F., … Conti,, E. (2010). Insights into the Recruitment of the NMD Machinery from the Crystal Structure of a Core EJC‐UPF3b Complex. Proceedings of the National Academy of Sciences of the United States of America, 107(22), 10050–10055.
Bühler,, M., Steiner,, S., Mohn,, F., Paillusson,, A., & Mühlemann,, O. (2006). EJC‐independent degradation of nonsense immunoglobulin‐mu mRNA depends on 3’ UTR length. Nature Structural %26 Molecular Biology, 13(5), 462–464.
Calin,, G. A., Dumitru,, C. D., Shimizu,, M., Bichi,, R., Zupo,, S., Noch,, E., … Croce, C. M. (2002). Frequent deletions and down‐regulation of micro‐RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences of the United States of America, 99(24), 15524–15529.
Calin,, G. A., Ferracin,, M., Cimmino,, A., Di Leva,, G., Shimizu,, M., Wojcik,, S. E., … Croce,, C. M. (2005). A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. The New England Journal of Medicine, 353(17), 1793–1801.
Causier,, B., Li,, Z., De Smet,, R., Lloyd,, J. P. B., Van de Peer,, Y., & Davies,, B. (2017). Conservation of nonsense‐mediated mRNA decay complex components throughout eukaryotic evolution. Scientific Reports, 7(1), 16692.
Celik,, A., Baker,, R., He,, F., & Jacobson,, A. (2017). High resolution profiling of NMD targets in yeast reveals translational fidelity as a basis for substrate selection. RNA, 23(5), 735–748. https://doi.org/10.1261/rna.060541.116
Chakrabarti,, S., Bonneau,, F., Schüssler,, S., Eppinger,, E., & Conti,, E. (2014). Phospho‐dependent and phospho‐independent interactions of the helicase UPF1 with the NMD factors SMG5‐SMG7 and SMG6. Nucleic Acids Research, 42(14), 9447–9460.
Chakrabarti,, S., Jayachandran,, U., Bonneau,, F., Fiorini,, F., Basquin,, C., Domcke,, S., … Conti,, E. (2011). Molecular mechanisms for the RNA‐dependent ATPase activity of Upf1 and its regulation by Upf2. Molecular Cell, 41(6), 693–703.
Chamieh,, H., Ballut,, L., Bonneau,, F., & Le Hir,, H. (2008). NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity. Nature Structural %26 Molecular Biology, 15(1), 85–93.
Chan,, W. K., Huang,, L., Gudikote,, J. P., Chang,, Y. F., Imam, J. S., MacLean, J. A., %26 Wilkinson, M. F. (2007). An alternative branch of the nonsense‐mediated decay pathway. The EMBO Journal, 26(4), 1820–1830. http://emboj.embopress.org/content/26/7/1820.abstract
Chapin,, A., Hu,, H., Rynearson,, S. G., Hollien,, J., Yandell,, M., & Metzstein,, M. M. (2014). In vivo determination of direct targets of the nonsense‐mediated decay pathway in drosophila. G3, 4(3), 485–496.
Chen,, G., Zhu,, W., Shi,, D., Lv,, L., Zhang,, C., Liu,, P., & Weixing,, H. (2010). MicroRNA‐181a sensitizes human malignant glioma U87MG Cells to radiation by targeting Bcl‐2. Oncology Reports, 23(4), 997–1003.
Cheng,, Z., Muhlrad,, D., Lim,, M. K., Parker,, R., & Song,, H. (2007). Structural and functional insights into the human Upf1 helicase core. The EMBO Journal, 26(1), 253–264.
Chester,, A., Somasekaram,, A., Tzimina,, M., Jarmuz,, A., Gisbourne,, J., O`Keefe,, R., … Navaratnam,, N. (2003). The apolipoprotein B mRNA editing complex performs a multifunctional cycle and suppresses nonsense‐mediated decay. The EMBO Journal, 22(15), 3971–3982.
Cho,, H., Kim,, K. M., & Kim,, Y. K. (2009). Human proline‐rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex. Molecular Cell, 33(1), 75–86.
Cimmino,, A., Calin,, G. A., Fabbri,, M., Iorio,, M. V., Ferracin,, M., Shimizu,, M., … Croce,, C. M. (2005). miR‐15 and miR‐16 induce apoptosis by targeting BCL2. Proceedings of the National Academy of Sciences of the United States of America, 102(39), 13944–13949.
Cleary,, M. L., Smith,, S. D., & Sklar,, J. (1986). Cloning and structural analysis of cDNAs for Bcl‐2 and a hybrid Bcl‐2/immunoglobulin transcript resulting from the T (14; 18) translocation. Cell, 47(1), 19–28.
Clerici,, M., Deniaud,, A., Boehm,, V., Gehring,, N. H., Schaffitzel,, C., & Cusack,, S. (2013). Structural and functional analysis of the three MIF4G domains of nonsense‐mediated decay factor UPF2. Nucleic Acids Research, 42(4), 2673‐2686. https://doi.org/10.1093/nar/gkt1197
Clerici,, M., Mourão,, A., Gutsche,, I., Gehring,, N. H., Hentze,, M. W., Kulozik,, A., … Cusack,, S. (2009). Unusual bipartite mode of interaction between the nonsense‐mediated decay factors, UPF1 and UPF2. The EMBO Journal, 28(15), 2293–2306.
Colombo,, M., Karousis,, E. D., Bourquin,, J., Bruggmann,, R., & Mühlemann,, O. (2016). Transcriptome‐wide identification of NMD‐targeted human mRNAs reveals extensive redundancy between SMG6‐ and SMG7‐mediated degradation pathways. RNA, 23(2), 189–201. https://doi.org/10.1261/rna.059055.116
Cui,, Y., Hagan,, K. W., Zhang,, S., & Peltz,, S. W. (1995). Identification and characterization of genes that are required for the accelerated degradation of mRNAs containing a premature translational termination codon. Genes %26 Development, 9(4), 423–436.
Culbertson,, M. R., Underbrink,, K. M., & Fink,, G. R. (1980). Frameshift suppression Saccharomyces cerevisiae. II. Genetic properties of group II suppressors. Genetics, 95(4), 833–853.
Czabotar,, P. E., Lessene,, G., Strasser,, A., & Adams,, J. M. (2014). Control of apoptosis by the BCL‐2 protein family: Implications for physiology and therapy. Nature Reviews Molecular Cell Biology, 15(1), 49–63.
Czaplinski,, K., Ruiz‐Echevarria,, M. J., Paushkin,, S. V., Han,, X., Weng,, Y., Perlick,, H. A., … Peltz,, S. W. (1998). The surveillance complex interacts with the translation release factors to enhance termination and degrade aberrant mRNAs. Genes %26 Development, 12(11), 1665–1677.
Czaplinski,, K., Weng,, Y., Hagan,, K. W., & Peltz,, S. W. (1995). Purification and characterization of the Upf1 protein: A factor involved in translation and mRNA degradation. RNA, 1(6), 610–623.
Dang,, Y., Low,, W.‐K., Xu,, J., Gehring,, N. H., Dietz,, H. C., Romo,, D., & Liu,, J. O. (2009). Inhibition of nonsense‐mediated mRNA decay by the natural product pateamine A through eukaryotic initiation factor 4AIII. The Journal of Biological Chemistry, 284(35), 23613–23621.
de Lima Morais,, D. A. & Harrison,, P. M. (2010). Large‐scale evidence for conservation of NMD candidature across mammals. PloS One, 5(7), e11695.
Degtiar,, E., Fridman,, A., Gottlieb,, D., Vexler,, K., Berezin,, I., Farhi,, R., … Shaul,, O. (2015). The feedback control of UPF3 Is crucial for RNA surveillance in plants. Nucleic Acids Research, 43(8), 4219–4235.
Dehecq,, M., Decourty,, L., Namane,, A., Proux,, C., Kanaan,, J., Le Hir,, H., … Saveanu,, C. (2018). Nonsense‐mediated mRNA decay involves two distinct Upf1‐bound complexes. The EMBO Journal, 37(21), e99278. https://doi.org/10.15252/embj.201899278
Deng,, J., Carlson,, N., Takeyama,, K., Cin,, P. D., Shipp,, M., & Letai,, A. (2007). BH3 profiling identifies three distinct classes of apoptotic blocks to predict response to ABT‐737 and conventional chemotherapeutic agents. Cancer Cell, 12(2), 171–185.
Diem,, M. D., Chan,, C. C., Younis,, I., & Dreyfuss,, G. (2007). PYM binds the cytoplasmic exon‐junction complex and ribosomes to enhance translation of spliced mRNAs. Nature Structural %26 Molecular Biology, 14(12), 1173–1179.
Doma,, M. K., & Parker,, R. (2007). RNA quality control in eukaryotes. Cell, 131(4), 660–668.
Durand,, S., Franks,, T. M., & Lykke‐Andersen,, J. (2016). Hyperphosphorylation amplifies UPF1 activity to resolve stalls in nonsense‐mediated mRNA decay. Nature Communications, 7, 12434.
Eberle,, A. B., Lykke‐Andersen,, S., Mühlemann,, O., & Jensen,, T. H. (2009). SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. Nature Structural %26 Molecular Biology, 16(1), 49–55.
Eberle,, A. B., Stalder,, L., Mathys,, H., Orozco,, R. Z., & Mühlemann,, O. (2008). Posttranscriptional gene regulation by spatial rearrangement of the 3′ untranslated region. PLoS Biology, 6(4), e92.
Eyler,, D. E., Wehner,, K. A., & Green,, R. (2013). Eukaryotic release factor 3 Is required for multiple turnovers of peptide release catalysis by eukaryotic release factor 1. The Journal of Biological Chemistry, 288(41), 29530–29538.
Fairman‐Williams,, M. E., Guenther,, U.‐P., & Jankowsky,, E. (2010). SF1 and SF2 helicases: Family matters. Current Opinion in Structural Biology, 20(3), 313–324.
Fiorini,, F., Bagchi,, D., Le Hir,, H., & Croquette,, V. (2015). Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities. Nature Communications, 6, 7581. https://doi.org/10.1038/ncomms8581
Fiorini,, F., Robin,, J.‐P., Kanaan,, J., Borowiak,, M., Croquette,, V., Le Hir,, H., … Mocquet,, V. (2018). HTLV‐1 tax plugs and freezes UPF1 helicase leading to nonsense‐mediated mRNA decay inhibition. Nature Communications, 9(1), 431.
Fontaine,, K. A., Leon,, K. E., Khalid,, M. M., Tomar,, S., Jimenez‐Morales,, D., Dunlap,, M., … Ott, M. (2018). The cellular NMD pathway restricts Zika virus infection and is targeted by the viral capsid protein. mBio, 9(6), e02126–18. https://doi.org/10.1128/mBio.02126-18
Franks,, T. M., Singh,, G., & Lykke‐Andersen,, J. (2010). Upf1 ATPase‐dependent mRNP disassembly is required for completion of nonsense‐ mediated mRNA decay. Cell, 143(6), 938–950.
Frolova,, L., Le Goff,, X., Zhouravleva,, G., Davydova,, E., Philippe,, M., & Kisselev,, L. (1996). Eukaryotic polypeptide chain release factor eRF3 is an eRF1‐ and ribosome‐dependent guanosine triphosphatase. RNA, 2(4), 334–341.
Frolova,, L. Y., Tsivkovskii,, R. Y., Sivolobova,, G. F., Oparina,, N. Y., Serpinsky,, O. I., Blinov,, V. M., … Kisselev,, L. L. (1999). Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger Peptidyl‐tRNA hydrolysis. RNA, 5(8), 1014–1020.
Gao,, Z., & Wilkinson,, M. (2017). An RNA decay factor wears a new coat: UPF3B modulates translation termination. F1000Research, 6, 2159.
Garcia‐Moreno,, M., Noerenberg,, M., Ni,, S., Järvelin,, A. I., González‐Almela,, E., Lenz,, C. E., … Castello, A. (2019). System‐wide profiling of RNA‐binding proteins uncovers key regulators of virus infection. Molecular Cell, 74(1), 196–211. https://doi.org/10.1016/j.molcel.2019.01.017
Gardner,, L. B. (2008). Hypoxic inhibition of nonsense‐mediated RNA decay regulates gene expression and the integrated stress response. Molecular and Cellular Biology, 28(11), 3729–3741.
Gardner,, L. B. (2010). Nonsense‐mediated RNA decay regulation by cellular stress: Implications for tumorigenesis. Molecular Cancer Research: MCR, 8(3), 295–308.
Gatfield,, D., & Izaurralde,, E. (2004). Nonsense‐mediated messenger RNA decay is initiated by endonucleolytic cleavage in drosophila. Nature, 429(6991), 575–578.
Ge,, Z., Quek,, B. L., Beemon,, K. L., & Hogg,, J. R. (2016). Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense‐mediated mRNA decay pathway. eLife, 5, e11155. https://doi.org/10.7554/eLife.11155
Gehring,, N. H., Kunz,, J. B., Neu‐Yilik,, G., Breit,, S., Viegas,, M. H., Hentze,, M. W., & Kulozik,, A. E. (2005). Exon‐junction complex components specify distinct routes of nonsense‐mediated mRNA decay with differential cofactor requirements. Molecular Cell, 20(1), 65–75.
Gehring,, N. H., Lamprinaki,, S., Hentze,, M. W., & Kulozik,, A. E. (2009). The hierarchy of exon‐junction complex assembly by the spliceosome explains key features of mammalian nonsense‐mediated mRNA decay. PLoS Biology, 7(5), e1000120.
Gehring,, N. H., Lamprinaki,, S., Kulozik,, A. E., & Hentze,, M. W. (2009). Disassembly of exon junction complexes by PYM. Cell, 137(3), 536–548.
Gehring,, N. H., Neu‐Yilik,, G., Schell,, T., Hentze,, M. W., & Kulozik,, A. E. (2003). Y14 and hUpf3b Form an NMD‐activating complex. Molecular Cell, 11(4), 939–949.
Goetz,, A. E., & Wilkinson,, M. (2017). Stress and the nonsense‐mediated RNA decay pathway. Cellular and Molecular Life Sciences, 74(19), 3509–3531.
Gowravaram,, M., Bonneau,, F., Kanaan,, J., Maciej,, V. D., Fiorini,, F., Raj,, S., … Chakrabarti,, S. (2018). A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform‐specific manner. Nucleic Acids Research, 46(5), 2648–2659. https://doi.org/10.1093/nar/gky040
Hamid,, F. M., & Makeyev,, E. V. (2014). Emerging functions of alternative splicing coupled with nonsense‐mediated decay. Biochemical Society Transactions, 42(4), 1168–1173.
Hauer,, C., Sieber,, J., Schwarzl,, T., Hollerer,, I., Curk,, T., Alleaume,, A.‐M., … Kulozik,, A. E. (2016). Exon junction complexes show a distributional bias toward alternatively spliced mRNAs and against mRNAs coding for ribosomal proteins. Cell Reports, 16(6), 1588–1603.
He,, F., & Jacobson,, A. (2015). Control of mRNA decapping by positive and negative regulatory elements in the Dcp2 C‐terminal domain. RNA, 21(9), 1633–1647.
Hogg,, J. R. (2011). This message was inspected by Upf1: 3’UTR length sensing in mRNA quality control. Cell Cycle, 10(3), 372–373.
Hogg,, J. R. (2016). Viral evasion and manipulation of host RNA quality control pathways. Journal of Virology, 90(16), 7010–7018. https://doi.org/10.1128/JVI.00607-16
Hogg,, J. R., & Goff,, S. P. (2010). Upf1 senses 3′ UTR length to potentiate mRNA decay. Cell, 143(3), 379–389.
Hoskins,, A. A. H., Friedman,, L. J. F., Gallagher,, S. S. G., Crawford,, D. J. C., Anderson,, E. G. A., Wombacher,, R. W., … Moore,, M. J. (2011). Ordered and dynamic assembly of single spliceosomes. Science, 331(6022), 1289–1295.
Hoskins,, A. A., Rodgers,, M. L., Friedman,, L. J., Gelles,, J., & Moore,, M. J. (2016). Single molecule analysis reveals reversible and irreversible steps during spliceosome activation. eLife, 5, e14166. https://doi.org/10.7554/eLife.14166
Huang,, L., Shum,, E. Y., Jones,, S. H., Lou,, C.‐H., Dumdie,, J., Kim,, H., … Wilkinson, M. F. (2017). A Upf3b‐mutant mouse model with behavioral and neurogenesis defects. Molecular Psychiatry, 23(8), 1773–1786. https://doi.org/10.1038/mp.2017.173
Huang,, L., Lou,, C.‐H., Chan,, W., Shum,, E. Y., Shao,, A., Stone,, E., … Wilkinson,, M. F. (2011). RNA homeostasis governed by cell type‐specific and branched feedback loops acting on NMD. Molecular Cell, 43(6), 950–961.
Huang,, P., Ye,, B., Yu,, Y., Shi,, J., & Zhao,, H. (2015). MicroRNA‐181 functions as a tumor suppressor in non‐small cell lung cancer (NSCLC) by targeting Bcl‐2. Tumour Biology, 36(5), 3381–3387.
Hug,, N., Longman,, D., & Cáceres,, J. F. (2016). Mechanism and regulation of the nonsense‐mediated decay pathway. Nucleic Acids Research, 44(4), 1483–1495. https://doi.org/10.1093/nar/gkw010
Hui,, J., Hung,, L.‐H., Heiner,, M., Schreiner,, S., Neumüller,, N., Reither,, G., … Bindereif,, A. (2005). Intronic CA‐repeat and CA‐rich elements: A new class of regulators of mammalian alternative splicing. The EMBO Journal, 24(11), 1988–1998.
Huntzinger,, E., Kashima,, I., Fauser,, M., Saulière,, J., & Izaurralde,, E. (2008). SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan. RNA, 14(12), 2609–2617.
Hurt,, J. A., Robertson,, A. D., & Burge,, C. B. (2013). Global analyses of UPF1 binding and function reveal expanded scope of nonsense‐mediated mRNA decay. Genome Research, 23(10), 1636–1650.
Hwang,, J., Sato,, H., Tang,, Y., Matsuda,, D., & Maquat, L. E. (2010). UPF1 association with the cap‐binding protein, CBP80, promotes nonsense‐mediated mRNA decay at two distinct steps. Molecular Cell, 39(3), 396–409.
Isken,, O., Kim,, Y. K., Hosoda,, N., Mayeur,, G. L., Hershey,, J. W. B., & Maquat,, L. E. (2008). Upf1 phosphorylation triggers translational repression during nonsense‐mediated mRNA decay. Cell, 133(2), 314–327.
Ivanov,, P. V., Gehring,, N. H., Kunz,, J. B., Hentze,, M. W., & Kulozik,, A. E. (2008). Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways. The EMBO Journal, 27(5), 736–747.
Jaffrey,, S. R., & Wilkinson,, M. F. (2018). Nonsense‐mediated RNA decay in the brain: Emerging modulator of neural development and disease. Nature Reviews Neuroscience, 19(12), 715–728. https://doi.org/10.1038/s41583-018-0079-z
Johansson,, M. J. O., & Jacobson,, A. (2010). Nonsense‐mediated mRNA decay maintains translational fidelity by limiting magnesium uptake. Genes %26 Development, 24(14), 1491–1495.
Kadlec,, J., Izaurralde,, E., & Cusack,, S. (2004). The structural basis for the interaction between nonsense‐mediated mRNA decay factors UPF2 and UPF3. Nature Structural %26 Molecular Biology, 11(4), 330–337.
Kanaan,, J., Raj,, S., Decourty,, L., Saveanu,, C., Croquette,, V., & Le Hir,, H. (2018). UPF1‐like helicase grip on nucleic acids dictates processivity. Nature Communications, 9(1), 3752.
Karam,, R., Lou,, C.‐H. H., Kroeger,, H., Huang,, L., Lin,, J. H., & Wilkinson,, M. F. (2015). The unfolded protein response is shaped by the NMD pathway. EMBO Reports, 16(5), 599–609.
Karousis,, E. D., & Mühlemann,, O. (2018). Nonsense‐mediated mRNA decay begins where translation ends. Cold Spring Harbor Perspectives in Biology, 11(2), a032862. https://doi.org/10.1101/cshperspect.a032862
Kashima,, I., Yamashita,, A., Izumi,, N., Kataoka,, N., Morishita,, R., Hoshino,, S., … Ohno,, S. (2006). Binding of a novel SMG‐1‐Upf1‐eRF1‐eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense‐mediated mRNA decay. Genes %26 Development, 20(3), 355–367.
Kataoka,, N. K., Yong,, J. Y., Kim,, V. N. K., Velazquez,, F. V., Perkinson,, R. A. P., Wang,, F. W., & Dreyfuss,, G. D. (2000). Pre‐mRNA splicing imprints mRNA in the nucleus with a Novel RNA‐binding protein that persists in the cytoplasm. Molecular Cell, 6(3), 673–682.
Kaygun,, H., & Marzluff,, W. F. (2005). Regulated degradation of replication‐dependent histone mRNAs requires both ATR and Upf1. Nature Structural %26 Molecular Biology, 12(9), 794–800.
Keeling,, K. M., Lanier,, J., Ming,, D., Salas‐Marco,, J., Lin,, G., Kaenjak‐Angeletti,, A., & Bedwell,, D. M. (2004). Leaky termination at premature stop codons antagonizes nonsense‐mediated mRNA decay in S. cerevisiae. RNA, 10(4), 691–703.
Kervestin,, S., Li,, C., Buckingham,, R., & Jacobson,, A. (2012). Testing the faux‐UTR model for NMD: Analysis of Upf1p and Pab1p competition for binding to eRF3/Sup35p. Biochimie, 94(7), 1560–1571.
Kim,, V. N., Kataoka,, N., & Dreyfuss,, G. (2001). Role of the nonsense‐mediated decay factor hUpf3 in the splicing‐dependent exon‐exon junction complex. Science, 293(5536), 1832–1836.
Kim,, V. N., Yong,, J., Kataoka,, N., Abel,, L., Diem,, M. D., & Dreyfuss,, G. (2001). The Y14 protein communicates to the cytoplasm the position of exon‐exon junctions. The EMBO Journal, 20(8), 2062–2068.
Kim,, Y. K., Furic,, L., DesGroseillers,, L., & Maquat,, L. E. (2005). Mammalian staufen1 recruits Upf1 to specific mRNA 3′ UTRs so as to elicit mRNA decay. Cell, 120(2), 195–208.
Kim,, Y. K., & Maquat,, L. E. (2019). UPFront and center in RNA decay: UPF1 in nonsense‐mediated mRNA decay and beyond. RNA, 25(4), 407–422. https://doi.org/10.1261/rna.070136.118
Kishor,, A., Ge,, Z., & Hogg,, J. R. (2019). hnRNP L‐dependent protection of normal mRNAs from NMD subverts quality control in B cell lymphoma. The EMBO Journal, 38(3), e99128.
Klein,, U., Lia,, M., Crespo,, M., Siegel,, R., Shen,, Q., Mo,, T., … Dalla‐Favera, R. (2010). The DLEU2/miR‐15a/16‐1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell, 17(1), 28–40.
Kunz,, J. B., Neu‐Yilik,, G., Hentze,, M. W., Kulozik,, A. E., & Gehring,, N. H. (2006). Functions of hUpf3a and hUpf3b in nonsense‐mediated mRNA decay and translation. RNA, 12(6), 1015–1022.
Kurosaki,, T., Li,, W., Hoque,, M., Popp,, M. W.‐L., Ermolenko,, D. N., Tian,, B., & Maquat,, L. E. (2014). A post‐translational regulatory switch on UPF1 controls targeted mRNA degradation. Genes %26 Development, 28(17), 1900–1916.
Kurosaki,, T., & Maquat,, L. E. (2013). Rules that govern UPF1 binding to mRNA 3’ UTRs. Proceedings of the National Academy of Sciences of the United States of America, 110(9), 3357–3362.
Lareau,, L. F., & Brenner,, S. E. (2015). Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. Molecular Biology and Evolution, 32(4), 1072–1079.
Lareau,, L. F., Inada,, M., Green,, R. E., Wengrod,, J. C., & Brenner,, S. E. (2007). Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature, 446(7138), 926–929.
Laumonnier,, F., Shoubridge,, C., Antar,, C., Nguyen,, L. S., Van Esch,, H., Kleefstra,, T., … Raynaud, M. (2010). Mutations of the UPF3B gene, which encodes a protein widely expressed in neurons, are associated with nonspecific mental retardation with or without autism. Molecular Psychiatry, 15(7), 767–776.
Le Hir,, H., Gatfield,, D., Izaurralde,, E., & Moore,, M. J. (2001). The exon‐exon junction complex provides a binding platform for factors involved in mRNA export and nonsense‐mediated mRNA decay. The EMBO Journal, 20(17), 4987–4997.
Le Hir,, H., Izaurralde,, E., Maquat,, L. E., & Moore,, M. J. (2000). The spliceosome deposits multiple proteins 20‐24 nucleotides upstream of mRNA exon‐exon junctions. The EMBO Journal, 19(24), 6860–6869.
Le Hir,, H., Moore,, M. J., & Maquat,, L. E. (2000). Pre‐mRNA splicing alters mRNP composition: Evidence for stable association of proteins at exon‐exon junctions. Genes %26 Development, 14(9), 1098–1108.
Le Hir,, H., Saulière,, J., & Wang,, Z. (2016). The exon junction complex as a node of post‐transcriptional networks. Nature Reviews Molecular Cell Biology, 17(1), 41–54.
Lee,, B. S., & Culbertson,, M. R. (1995). Identification of an additional gene required for eukaryotic nonsense mRNA turnover. Proceedings of the National Academy of Sciences of the United States of America, 92(22), 10354–10358.
Lee,, D.‐H., Lim,, M.‐H., Youn,, D.‐Y., Jung,, S. E., Ahn,, Y. S., Tsujimoto,, Y., & Lee,, J.‐H. (2009). hnRNP L binds to CA repeats in the 3′ UTR of Bcl‐2 mRNA. Biochemical and Biophysical Research Communications, 382(3), 583–587.
Lee,, S. R., Pratt,, G. A., Martinez,, F. J., Yeo,, G. W., & Lykke‐Andersen,, J. (2015). Target discrimination in nonsense‐mediated mRNA decay requires Upf1 ATPase activity. Molecular Cell, 59(3), 413–425.
Leeds,, P., Wood,, J. M., Lee,, B. S., & Culbertson,, M. R. (1992). Gene products that promote mRNA turnover in saccharomyces cerevisiae. Molecular and Cellular Biology, 12(5), 2165–2177.
Leich,, E., Ott,, G., & Rosenwald,, A. (2011). Pathology, pathogenesis and molecular genetics of follicular NHL. Best Practice %26 Research Clinical Haematology, 24(2), 95–109.
Lloyd,, J. P. B. (2018). The evolution and diversity of the nonsense‐mediated mRNA decay pathway. F1000Research, 7, 1299. https://doi.org/10.12688/f1000research.15872.1
Loh,, B., Jonas,, S., & Izaurralde,, E. (2013). The SMG5‐SMG7 heterodimer directly recruits the CCR4‐NOT deadenylase complex to mRNAs containing nonsense codons via interaction with POP2. Genes %26 Development, 27(19), 2125–2138.
López‐Perrote,, A., Castaño,, R., Melero,, R., Zamarro,, T., Kurosawa,, H., Ohnishi,, T., … Llorca, O. (2016). Human nonsense‐mediated mRNA decay factor UPF2 interacts directly with eRF3 and the SURF complex. Nucleic Acids Research, 44(4), 1909–1923. https://doi.org/10.1093/nar/gkv1527
Losson,, R., & Lacroute,, F. (1979). Interference of nonsense mutations with eukaryotic messenger RNA stability. Proceedings of the National Academy of Sciences of the United States of America, 76(10), 5134–5137.
Lykke‐Andersen,, J., Shu,, M. D., & Steitz,, J. A. (2000). Human Upf proteins target an mRNA for nonsense‐mediated decay when bound downstream of a termination codon. Cell, 103(7), 1121–1131.
Lynch,, S. A., Nguyen,, L. S., Ng,, L. Y., Waldron,, M., McDonald,, D., & Gecz,, J. (2012). Broadening the phenotype associated with mutations in UPF3B: Two further cases with renal dysplasia and variable developmental delay. European Journal of Medical Genetics, 55(8‐9), 476–479.
Mabin,, J. W., Woodward,, L. A., Patton,, R. D., Yi,, Z., Jia,, M., Wysocki,, V. H., … Singh,, G. (2018). The exon junction complex undergoes a compositional switch that alters mRNP structure and nonsense‐mediated mRNA decay activity. Cell Reports, 25(9), 2431–2446.
Maquat,, L. E., Kinniburgh,, A. J., Rachmilewitz,, E. A., & Ross,, J. (1981). Unstable beta‐globin mRNA in mRNA‐deficient beta O thalassemia. Cell, 27(3 Pt 2), 543–553.
Matsuda,, D., Hosoda,, N., Kim,, Y. K., & Maquat,, L. E. (2007). Failsafe nonsense‐mediated mRNA decay does not detectably target eIF4E‐bound mRNA. Nature Structural %26 Molecular Biology, 14(10), 974–979.
May,, J. P., Yuan,, X., Sawicki,, E., & Simon,, A. E. (2018). RNA virus evasion of nonsense‐mediated decay. PLoS Pathogens, 14(11), e1007459.
Mayr,, C. (2016). Evolution and biological roles of alternative 3’UTRs. Trends in Cell Biology, 26(3), 227–237.
McGlincy,, N. J., & Smith,, C. W. J. (2008). Alternative splicing resulting in nonsense‐mediated mRNA decay: What is the meaning of nonsense? Trends in Biochemical Sciences, 33(8), 385–393.
McIlwain,, D. R., Pan,, Q., Reilly,, P. T., Elia,, A. J., McCracken,, S., Wakeham,, A. C., … Mak,, T. W. (2010). Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense‐mediated mRNA decay. Proceedings of the National Academy of Sciences of the United States of America, 107(27), 12186–12191.
Meaux,, S., van Hoof,, A., & Baker,, K. E. (2008). Nonsense‐mediated mRNA decay in yeast does not require PAB1 or a poly(A) tail. Molecular Cell, 29(1), 134–140.
Medghalchi,, S. M., Frischmeyer,, P. A., Mendell,, J. T., Kelly,, A. G., Lawler,, A. M., & Dietz,, H. C. (2001). Rent1, a trans‐effector of nonsense‐mediated mRNA decay, is essential for mammalian embryonic viability. Human Molecular Genetics, 10(2), 99–105.
Melero,, R., Buchwald,, G., Castaño,, R., Raabe,, M., Gil,, D., Lázaro,, M., … Llorca,, O. (2012). The cryo‐EM structure of the UPF–EJC complex shows UPF1 poised toward the RNA 3′ end. Nature Structural %26 Molecular Biology, 19, 498.
Mendell,, J. T., Sharifi,, N. A., Meyers,, J. L., Martinez‐Murillo,, F., & Dietz,, H. C. (2004). Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nature Genetics, 36(10), 1073–1078.
Metze,, S., Herzog,, V. A., Ruepp,, M.‐D., & Mühlemann,, O. (2013). Comparison of EJC‐enhanced and EJC‐independent NMD in human cells reveals two partially redundant degradation pathways. RNA, 19(10), 1432–1448.
Metzstein,, M. M., & Krasnow,, M. A. (2006). Functions of the nonsense‐mediated mRNA decay pathway in drosophila development. PLoS Genetics, 2(12), e180.
Mino,, T., Murakawa,, Y., Fukao,, A., Vandenbon,, A., Wessels,, H.‐H., Ori,, D., … Takeuchi, O. (2015). Regnase‐1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms. Cell, 161(5), 1058–1073.
Mühlemann,, O., & Jensen,, T. H. (2012). mRNP quality control goes regulatory. Trends in Genetics, 28(2), 70–77.
Nagy,, E., & Maquat,, L. E. (1998). A rule for termination‐codon position within intron‐containing genes: When nonsense affects RNA abundance. Trends in Biochemical Sciences, 23(6), 198–199.
Nelson,, J. O., Moore,, K. A., Chapin,, A., Hollien,, J., & Metzstein,, M. M. (2016). Degradation of Gadd45 mRNA by nonsense‐mediated decay is essential for viability. eLife, 5, e12876. https://doi.org/10.7554/eLife.12876
Neu‐Yilik,, G., Raimondeau,, E., Eliseev,, B., Yeramala,, L., Amthor,, B., Deniaud,, A., … Kulozik, A. E. (2017). Dual function of UPF3B in early and late translation termination. The EMBO Journal, 36(20), 2968–2986. https://doi.org/10.15252/embj.201797079
Ni,, J. Z., Grate,, L., Donohue,, J. P., Preston,, C., Nobida,, N., O`Brien,, G., … Jr,, M. A. (2007). Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense‐mediated decay. Genes %26 Development, 21(6), 708–718.
Nicholson,, P., Gkratsou,, A., Josi,, C., Colombo,, M., & Mühlemann,, O. (2018). Dissecting the functions of SMG5, SMG7 and PNRC2 in nonsense‐mediated mRNA decay of human cells. RNA, 24(4), 557–573. https://doi.org/10.1261/rna.063719.117
Nicholson,, P., Joncourt,, R., & Mühlemann,, O. (2012). Analysis of nonsense‐mediated mRNA decay in mammalian cells. Current Protocols in Cell Biology, 55(1), 27.4.1–27.4.61. https://doi.org/10.1002/0471143030.cb2704s55
Nicholson,, P., Josi,, C., Kurosawa,, H., Yamashita,, A., & Mühlemann,, O. (2014). A novel phosphorylation‐independent interaction between SMG6 and UPF1 is essential for human NMD. Nucleic Acids Research, 42(14), 9217–9235. https://doi.org/10.1093/nar/gku645
Ohnishi,, T., Yamashita,, A., Kashima,, I., Schell,, T., Anders,, K. R., Grimson,, A., … Ohno,, S. (2003). Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG‐5 and hSMG‐7. Molecular Cell, 12(5), 1187–1200.
Okada‐Katsuhata,, Y., Yamashita,, A., Kutsuzawa,, K., Izumi,, N., Hirahara,, F., & Ohno,, S. (2011). N‐ and C‐terminal Upf1 phosphorylations create binding platforms for SMG‐6 and SMG‐5:SMG‐7 during NMD. Nucleic Acids Research, 40(3), 1251–1266.
Ottens,, F., Boehm,, V., Sibley,, C. R., Ule,, J., & Gehring,, N. H. (2017). Transcript‐specific characteristics determine the contribution of endo‐ and exonucleolytic decay pathways during the degradation of nonsense‐mediated decay substrates. RNA, 23(8), 1224–1236.
Ouyang,, Y.‐B., Lu,, Y., Yue,, S., & Giffard,, R. G. (2012). miR‐181 targets multiple Bcl‐2 family members and influences apoptosis and mitochondrial function in astrocytes. Mitochondrion, 12(2), 213–219.
Pal,, M., Ishigaki,, Y., Nagy,, E., & Maquat,, L. E. (2001). Evidence that phosphorylation of human Upfl protein varies with intracellular location and is mediated by a wortmannin‐sensitive and rapamycin‐sensitive PI 3‐kinase‐related kinase signaling pathway. RNA, 7(1), 5–15.
Peixeiro,, I., Inácio,, Â., Barbosa,, C., Silva,, A. L., Liebhaber,, S. A., & Romão,, L. (2012). Interaction of PABPC1 with the translation initiation complex is critical to the NMD resistance of AUG‐proximal nonsense mutations. Nucleic Acids Research, 40(3), 1160–1173.
Pérez,, I., McAfee,, J. G., & Patton,, J. G. (1997). Multiple RRMs contribute to RNA binding specificity and affinity for polypyrimidine tract binding protein. Biochemistry, 36(39), 11881–11890.
Pisarev,, A. V., Skabkin,, M. A., Pisareva,, V. P., Skabkina,, O. V., Rakotondrafara,, A. M., Hentze,, M. W., … Pestova,, T. V. (2010). The Role of ABCE1 in eukaryotic posttermination ribosomal recycling. Molecular Cell, 37(2), 196–210.
Pisareva,, V. P., Skabkin,, M. A., Hellen,, C. U. T., Pestova,, T. V., & Pisarev,, A. V. (2011). Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80s ribosomes and stalled elongation complexes. The EMBO Journal, 30(9), 1804–1817.
Popp,, M. W.‐L., & Maquat,, L. E. (2013). Organizing principles of mammalian nonsense‐mediated mRNA decay. Annual Review of Genetics, 47, 139–165.
Raimondeau,, E., Bufton,, J. C., & Schaffitzel,, C. (2018). New insights into the interplay between the translation machinery and nonsense‐mediated mRNA decay factors. Biochemical Society Transactions, 46(3), 503–512. https://doi.org/10.1042/BST20170427
Rebbapragada,, I., & Lykke‐Andersen,, J. (2009). Execution of nonsense‐mediated mRNA decay: what defines a substrate? Current Opinion in Cell Biology, 21(3), 394–402.
Rehwinkel,, J., Letunic,, I., Raes,, J., Bork,, P., & Izaurralde,, E. (2005). Nonsense‐mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA, 11(10), 1530–1544.
Roque,, S., Cerciat,, M., Gaugué,, I., Mora,, L., Floch,, A. G., de Zamaroczy,, M., … Kervestin,, S. (2015). Interaction between the poly(A)‐binding protein Pab1 and the eukaryotic release factor eRF3 regulates translation termination but not mRNA decay in saccharomyces cerevisiae. RNA, 21(1), 124–134.
Sabirzhanov,, B., Zhao,, Z., Stoica,, B. A., Loane,, D. J., Wu,, J., Borroto,, C., … Faden,, A. I. (2014). Downregulation of miR‐23a and miR‐27a following experimental traumatic brain injury induces neuronal cell death through activation of proapoptotic Bcl‐2 proteins. The Journal of Neuroscience, 34(30), 10055–10071.
Salas‐Marco,, J., & Bedwell,, D. M. (2004). GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination. Molecular and Cellular Biology, 24(17), 7769–7778.
Schaefke,, B., Sun,, W., Li,, Y.‐S., Fang,, L., & Chen,, W. (2018). The evolution of posttranscriptional regulation. WIREs RNA, 9, e1485.
Schuetz,, J. M., Johnson,, N. A., Morin,, R. D., Scott,, D. W., Tan,, K., Ben‐Nierah,, S., … Gascoyne, R. D. (2012). BCL2 mutations in diffuse large B‐Cell lymphoma. Leukemia, 26(6), 1383–1390.
Schuller,, A. P., Zinshteyn,, B., Enam,, S. U., & Green,, R. (2018). Directed hydroxyl radical probing reveals Upf1 binding to the 80S ribosomal E site rRNA at the L1 stalk. Nucleic Acids Research, 46(4), 2060–2073.
Serdar,, L. D., Whiteside,, D. L., & Baker,, K. E. (2016). ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons. Nature Communications, 7, 14021.
Serin,, G., Gersappe,, A., Black,, J. D., Aronoff,, R., & Maquat,, L. E. (2001). Identification and characterization of human orthologues to saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG‐4). Molecular and Cellular Biology, 21(1), 209–223.
Seto,, M. (2002). Molecular mechanisms of lymphomagenesis through transcriptional disregulation by chromosome translocation. International Journal of Hematology, 76(Suppl 1), 323–326.
Shoemaker,, C. J., & Green,, R. (2011). Kinetic analysis reveals the ordered coupling of translation termination and ribosome recycling in yeast. Proceedings of the National Academy of Sciences of the United States of America, 108(51), E1392–E1398.
Shum,, E. Y., Jones,, S. H., Shao,, A., Dumdie,, J., Krause,, M. D., Chan,, W.‐K., … Wilkinson, M. F. (2016). The antagonistic gene paralogs Upf3a and Upf3b govern nonsense‐mediated RNA decay. Cell, 165(2), 382–395. https://doi.org/10.1016/j.cell.2016.02.046
Singh,, G., Pratt,, G., Yeo,, G. W., & Moore,, M. J. (2015). The clothes make the mRNA: Past and present trends in mRNP fashion. Annual Review of Biochemistry, 84, 325–354.
Singh,, G., Rebbapragada,, I., & Lykke‐Andersen,, J. (2008). A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense‐mediated mRNA decay. PLoS Biology, 6(4), e111.
Smith,, J. E., & Baker,, K. E. (2015). Nonsense‐mediated RNA decay—A switch and dial for regulating gene expression. BioEssays, 37(6), 612–623.
Sundararaman,, B., Zhan,, L., Blue,, S. M., Stanton,, R., Elkins,, K., Olson,, S., … Yeo, G. W. (2016). Resources for the comprehensive discovery of functional RNA elements. Molecular Cell, 61(6), 903–913.
Swisher,, K. D., & Parker,, R. (2011). Interactions between Upf1 and the decapping factors Edc3 and Pat1 in saccharomyces cerevisiae. PloS One, 6(10), e26547.
Szyszka,, P., Sharp,, S. I., Dedman,, A., Gurling,, H. M. D., & McQuillin,, A. (2012). A nonconservative amino acid change in the UPF3B gene in a patient with schizophrenia. Psychiatric Genetics, 22(3), 150–151.
Tang,, X., Zhu,, Y., Baker,, S. L., Bowler,, M. W., Chen,, B. J., Chen,, C., … Song,, H. (2016). Structural basis of suppression of host translation termination by moloney murine leukemia virus. Nature Communications, 7, 12070.
Tani,, H., Imamachi,, N., Salam,, K. A., Mizutani,, R., Ijiri,, K., Irie,, T., … Akimitsu,, N. (2012). Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability. RNA Biology, 9(11), 1370–1379.
Tarpey,, P. S., Raymond,, F. L., Nguyen,, L. S., Rodriguez,, J., Hackett,, A., Vandeleur,, L., … Gecz, J. (2007). Mutations in UPF3B, a member of the nonsense‐mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation. Nature Genetics, 39(9), 1127–1133.
Unterholzner,, L., & Izaurralde,, E. (2004). SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. Molecular Cell, 16(4), 587–596.
Vexler,, K., Cymerman,, M. A., Berezin,, I., Fridman,, A., Golani,, L., Lasnoy,, M., … Shaul,, O. (2016). The arabidopsis NMD factor UPF3 is feedback‐regulated at multiple levels and plays a role in plant response to salt stress. Frontiers in Plant Science, 7, 1376.
Wada,, M., Lokugamage,, K. G., Nakagawa,, K., Narayanan,, K., & Makino,, S. (2018). Interplay between coronavirus, a cytoplasmic RNA virus, and nonsense‐mediated mRNA decay pathway. Proceedings of the National Academy of Sciences of the United States of America, 115(43), E10157–E10166. https://doi.org/10.1073/pnas.1811675115
Wang,, H., Li,, J., Chi,, H., Zhang,, F., Zhu,, X., Cai,, J., & Yang,, X. (2015). MicroRNA‐181c targets Bcl‐2 and regulates mitochondrial morphology in myocardial cells. Journal of Cellular and Molecular Medicine, 19(9), 2084–2097.
Wang,, W., Czaplinski,, K., Rao,, Y., & Peltz,, S. W. (2001). The role of upf proteins in modulating the translation read‐through of nonsense‐containing transcripts. The EMBO Journal, 20(4), 880–890.
Wei,, C., Li,, L., & Gupta,, S. (2014). NF‐κB‐mediated miR‐30b regulation in cardiomyocytes cell death by targeting Bcl‐2. Molecular and Cellular Biochemistry, 387(1‐2), 135–141.
Weil,, J. E., & Beemon,, K. L. (2006). A 3’ UTR sequence stabilizes termination codons in the unspliced RNA of Rous sarcoma virus. RNA, 12(1), 102–110.
Weischenfeldt,, J., Damgaard,, I., Bryder,, D., Theilgaard‐Mönch,, K., Thoren,, L. A., Nielsen,, F. C., … Porse,, B. T. (2008). NMD is essential for hematopoietic stem and progenitor cells and for eliminating by‐products of programmed DNA rearrangements. Genes %26 Development, 22(10), 1381–1396.
Weng,, Y., Czaplinski,, K., & Peltz,, S. W. (1998). ATP is a cofactor of the Upf1 protein that modulates its translation termination and RNA binding activities. RNA, 4(2), 205–214.
Wittkopp,, N., Huntzinger,, E., Weiler,, C., Saulière,, J., Schmidt,, S., Sonawane,, M., & Izaurralde,, E. (2009). Nonsense‐mediated mRNA decay effectors are essential for zebrafish embryonic development and survival. Molecular and Cellular Biology, 29(13), 3517–3528.
Woodward,, L. A., Mabin,, J. W., Gangras,, P., & Singh,, G. (2016). The exon junction complex: A lifelong guardian of mRNA fate. WIREs RNA, 8(3), e1411. https://doi.org/10.1002/wrna.1411
Xu,, X., Zhang,, L., Tong,, P., Xun,, G., Su,, W., Xiong,, Z., … Hu, Z. (2013). Exome sequencing identifies UPF3B as the causative gene for a Chinese non‐syndrome mental retardation pedigree. Clinical Genetics, 83(6), 560–564.
Yepiskoposyan,, H., Aeschimann,, F., Nilsson,, D., Okoniewski,, M., & Muhlemann,, O. (2011). Autoregulation of the nonsense‐mediated mRNA decay pathway in human cells. RNA, 17(12), 2108–2118.
Zhong,, X., Zheng,, L., Shen,, J., Zhang,, D., Xiong,, M., Zhang,, Y., & Zhang, L. (2016). Suppression of microRNA 200 family expression by oncogenic KRAS activation promotes cell survival and epithelial‐mesenchymal transition in KRAS‐driven cancer. Molecular and Cellular Biology, 36(21), 2742–2754.
Zünd,, D., Gruber,, A. R., Zavolan,, M., & Mühlemann,, O. (2013). Translation‐dependent displacement of UPF1 from coding sequences causes its enrichment in 3’ UTRs. Nature Structural %26 Molecular Biology, 20(8), 936–943.