Quality control of eukaryotic mRNA: Safeguarding cells from abnormal mRNA function

Genes and Development

Volumn 21, Issue 15, 2007, Pages 1833-1856

  Isken, Olaf ^a   Maquat, Lynne E ^a  

^a UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

mRNA surveillance; No go mRNA decay; Nonsense mediated mRNA decay; Nonsense mediated transcriptional gene silencing; Nonstop mRNA decay

Indexed keywords

MESSENGER RNA;

3' UNTRANSLATED REGION; BIOGENESIS; CAENORHABDITIS ELEGANS; CELL NUCLEUS; CELL PROTECTION; CODON; CYTOPLASM; DOWNSTREAM PROCESSING; DROSOPHILA MELANOGASTER; EUKARYOTE; EVOLUTION; FLAGELLATE; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE SILENCING; GENE STRUCTURE; GENE TARGETING; GENETIC TRANSCRIPTION; HUMAN; INTRON; MAMMAL; MAMMAL CELL; MOLECULAR RECOGNITION; NONHUMAN; OOMYCETES; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN SYNTHESIS; QUALITY CONTROL; REVIEW; RNA SPLICING; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; SPLICEOSOME; STOP CODON;

ALTERNATIVE SPLICING; ANIMALS; CODON, NONSENSE; CODON, TERMINATOR; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENE SILENCING; HUMANS; MAMMALS; MODELS, GENETIC; MUTATION; PEPTIDE CHAIN ELONGATION, TRANSLATIONAL; PROTEIN BIOSYNTHESIS; RNA STABILITY; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE;

EUKARYOTA;

EID: 34547623918     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.1566807     Document Type: Review

References (259)

1. Akimitsu, N., Tanaka, J., and Pelletier, J. 2007. Translation of nonSTOP mRNA is repressed post-initiation in mammalian cells. EMBO J. 26: 2327-2338.
2. Alkalaeva, E.Z., Pisarev, A.V., Frolova, L.Y., Kisselev, L.L., and Pestova, T.V. 2006. In vitro reconstitution of translation reveals cooperativity between eukaryotic release factors eRF1 and eRF3. Cell 25: 1125-1136.
3. Amrani, N., Ganesan, R., Kervestin, S., Mangus, D.A., Ghosh, S., and Jacobson, A. 2004. A faux 3′-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay. Nature 432: 112-118.
4. Amrani, N., Sachs, M.S., and Jacobson, A. 2006. Early nonsense: mRNA decay solves a translational problem. Nat. Rev. Mol. Cell Biol. 7: 415-425.
5. Anders, K.R., Grimson, A., and Anderson, P. 2003. SMG-5, required for C. elegans nonsense-mediated mRNA decay, associates with SMG-2 and protein phosphatase 2A. EMBO J. 22: 641-650.
6. Andersen, C.B., Ballut, L., Johansen, J.S., Chamieh, H., Nielsen, K.H., Oliveira, C.L., Pedersen, J.S., Seraphin, B., Le Hir, H., and Andersen, G.R. 2006. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science 313: 1968-1972.
7. Araki, Y., Takahashi, S., Kobayashi, T., Kajiho, H., Hoshino, S., and Katada, T. 2001. Ski7p G protein interacts with the exosome and the Ski complex for 3′-to-5′ mRNA decay in yeast. EMBO J. 20: 4684-4693.
8. Arciga-Reyes, L., Wootton, L., Kieffer, M., and Davies, B. 2006. UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis. Plant J. 47: 480-489.
9. Bachi, A., Braun, I.C., Rodrigues, J.P., Pante, N., Ribbeck, K., von Kobbe, C., Kutay, U., Wilm, M., Gorlich, D., Carmo-Fonseca, M., et al. 2000. The C-terminal domain of TAP interacts with the nuclear pore complex and promotes export of specific CTE-bearing RNA substrates. RNA 6: 136-158.
10. Baek, D. and Green, P. 2005. Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc. Natl. Acad. Sci. 102: 12813-12818.
11. Baker, K.E. and Parker, R. 2004. Nonsense-mediated mRNA decay: Terminating erroneous gene expression. Curr. Opin. Cell Biol. 16: 293-299.
12. Baker, K.E. and Parker, R. 2006. Conventional 3′ end formation is not required for NMD substrate recognition in Saccharomyces cerevisiae. RNA 12: 1441-1445.
13. Ballut, L., Marchadier, B., Baguet, A., Tomasetto, C., Seraphin, B., and Le Hir, H. 2005. The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity. Nat. Struct. Mol. Biol. 12: 861-869.
14. Bateman, J.F., Freddi, S., Nattrass, G., and Savarirayan, R. 2003. Tissue-specific RNA surveillance? Nonsense-mediated mRNA decay causes collagen X haploinsufficiency in Schmid metaphyseal chondrodysplasia cartilage. Hum. Mol. Genet. 12: 217-225.
15. Behm-Ansmant, I. and Izaurralde, E. 2006. Quality control of gene expression: A stepwise assembly pathway for the surveillance complex that triggers nonsense-mediated mRNA decay. Genes & Dev. 20: 391-398.
16. Behm-Ansmant, I., Gatfield, D., Rehwinkel, J., Hilgers, V., and Izaurralde, E. 2007a. A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay. EMBO J. 26: 1591-1601.
17. Behm-Ansmant, I., Kashima, I., Rehwinkel, J., Sauliére, J., Wittkopp, N., and Izaurralde, E. 2007b. mRNA quality control: An ancient machinery recognizes and degrades mRNAs with nonsense codons. FEBS Lett. 581: 2845-2853.
18. Belgrader, P., Cheng, J., Zhou, X., Stephenson, L.S., and Maquat, L.E. 1994. Mammalian nonsense codons can be cis effectors of nuclear mRNA half-life. Mol. Cell. Biol. 14: 8219-8228.
19. Bhattacharya, A., Czaplinski, K., Trifillis, P., He, F., Jacobson, A., and Peltz, S.W. 2000. Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay. RNA 6: 1226-1235.
20. Bono, F., Ebert, J., Unterholzner, L., Guttler, T., Izaurralde, E., and Conti, E. 2004. Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex. EMBO Rep. 5: 304-310.
21. Bono, F., Ebert, J., Lorentzen, E., and Conti, E. 2006. The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell 126: 713-725.
22. Bremer, K.A., Stevens, A., and Schoenberg, D.R. 2003. An endonuclease activity similar to Xenopus PMR1 catalyzes the degradation of normal and nonsense-containing human β-globin mRNA in erythroid cells. RNA 9: 1157-1167.
23. Brouwer, R., Allmang, C., Raijmakers, R., van Aarssen, Y., Egberts, W.V., Petfalski, E., van Venrooij, W.J., Tollervey, D., and Pruijn, G.J. 2001. Three novel components of the human exosome. J. Biol. Chem. 276: 6177-6184.
24. Brumbaugh, K.M., Otterness, D.M., Geisen, C., Oliveira, V., Brognard, J., Li, X., Lejeune, F., Tibbetts, R.S., Maquat, L.E., and Abraham, R.T. 2004. The mRNA surveillance protein hSMG-1 functions in genotoxic stress response pathways in mammalian cells. Mol. Cell 14: 585-598.
25. Bühler, M., Wilkinson, M.F., and Mühlemann, O. 2002. Intranuclear degradation of nonsense codon-containing mRNA. EMBO Rep. 3: 646-651.
26. Bühler, M., Paillusson, A., and Mühlemann, O. 2004. Efficient downregulation of immunoglobulin μ mRNA with premature translation- termination codons requires the 5′-half of the VDJ exon. Nucleic Acids Res. 32: 3304-3315.
27. Bühler, M., Mohn, F., Stalder, L., and Mühlemann, O. 2005. Transcriptional silencing of nonsense codon-containing immunoglobulin minigenes. Mol. Cell 18: 307-317.
28. Bühler, M., Steiner, S., Mohn, F., Paillusson, A., and Mühlemann, O. 2006. EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3′ UTR length. Nat. Struct. Mol. Biol. 13: 462-464.
29. Cali, B.M., Kuchma, S.L., Latham, J., and Anderson, P. 1999. smg-7 is required for mRNA surveillance in Caenorhabditis elegans. Genetics 151: 605-616.
30. Cao, D. and Parker, R. 2003. Computational modeling and experimental analysis of nonsense-mediated decay in yeast. Cell 113: 533-545.
31. Caputi, M., Kendzior Jr., R.J., and Beemon, K.L. 2002. A nonsense mutation in the fibrillin-1 gene of a Marfan syndrome patient induces NMD and disrupts an exonic splicing enhancer. Genes & Dev. 16: 1754-1759.
32. Carr-Schmid, A., Pfund, C., Craig, E.A., and Kinzy, T.G. 2002. Novel G-protein complex whose requirement is linked to the translational status of the cell. Mol. Cell. Biol. 22: 2564-2574.
33. Cartegni, L. and Krainer, A.R. 2002. Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat. Genet. 30: 377-384.
34. Carter, M.S., Li, S., and Wilkinson, M.F. 1996. A splicing-dependent regulatory mechanism that detects translation signals. EMBO J. 15: 5965-5975.
35. Chan, C.C., Dostie, J., Diem, M.D., Feng, W., Mann, M., Rappsilber, J., and Dreyfuss, G. 2004. eIF4A3 is a novel component of the exon junction complex. RNA 10: 200-209.
36. Chan, W.K., Huang, L., Gudikote, J.P., Chang, Y.F., Imam, J.S., MacLean II, J.A., and Wilkinson, M.F. 2007. An alternative branch of the nonsense-mediated decay pathway. EMBO J. 26: 1820-1830.
37. Chang, Y.F., Imam, J.S., and Wilkinson, M.F. 2007. The nonsense-mediated decay RNA surveillance pathway. Annu. Rev. Biochem. 76: 51-74.
38. Chen, C.Y., Gherzi, R., Ong, S.E., Chan, E.L., Raijmakers, R., Pruijn, G.J., Stoecklin, G., Moroni, C., Mann, M., and Karin, M. 2001. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107: 451-464.
39. Chen, Z., Smith, K.R., Batterham, P., and Robin, C. 2005. Smg1 nonsense mutations do not abolish nonsense-mediated mRNA decay in Drosophila melanogaster. Genetics 171: 403-406.
40. Cheng, J. and Maquat, L.E. 1993. Nonsense codons can reduce the abundance of nuclear mRNA without affecting the abundance of pre-mRNA or the half-life of cytoplasmic mRNA. Mol. Cell. Biol. 13: 1892-1902.
41. Cheng, J., Belgrader, P., Zhou, X., and Maquat, L.E. 1994. Introns are cis effectors of the nonsense-codon-mediated reduction in nuclear mRNA abundance. Mol. Cell. Biol. 14: 6317-6325.
42. Cheng, Z., Muhlrad, D., Lim, M.K., Parker, R., and Song, H. 2007. Structural and functional insights into the human Upf1 helicase core. EMBO J. 26: 253-264.
43. Chester, A., Somasekaram, A., Tzimina, M., Jarmuz, A., Gisbourne, J., O'Keefe, R., Scott, J., and Navaratnam, N. 2003. The apolipoprotein B mRNA editing complex performs a multifunctional cycle and suppresses nonsense-mediated decay. EMBO J. 22: 3971-3982.
44. Chiu, S.Y., Serin, G., Ohara, O., and Maquat, L.E. 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: 77-87.
45. Chiu, S.Y., Lejeune, F., Ranganathan, A.C., and Maquat, L.E. 2004. The pioneer translation initiation complex is functionally distinct from but structurally overlaps with the steadystate translation initiation complex. Genes & Dev. 18: 745-754.
46. Coller, J. and Parker, R. 2004. Eukaryotic mRNA decapping. Annu. Rev. Biochem. 73: 861-890.
47. Coller, J.M., Gray, N.K., and Wickens, M.P. 1998. mRNA stabilization by poly(A) binding protein is independent of poly(A) and requires translation. Genes & Dev. 12: 3226-3235.
48. Collins, L. and Penny, D. 2005. Complex spliceosomal organization ancestral to extant eukaryotes. Mol. Biol. Evol. 22: 1053-1066.
49. Conti, E. and Izaurralde, E. 2005. Nonsense-mediated mRNA decay: Molecular insights and mechanistic variations across species. Curr. Opin. Cell Biol. 17: 316-325.
50. Couttet, P. and Grange, T. 2004. Premature termination codons enhance mRNA decapping in human cells. Nucleic Acids Res. 32: 488-494.
51. Cuccurese, M., Russo, G., Russo, A., and Pietropaolo, C. 2005. Alternative splicing and nonsense-mediated mRNA decay regulate mammalian ribosomal gene expression. Nucleic Acids Res. 33: 5965-5977.
52. Cui, Y. and Denis, C.L. 2003. In vivo evidence that defects in the transcriptional elongation factors RPB2, TFIIS, and SPT5 enhance upstream poly(A) site utilization. Mol. Cell. Biol. 23: 7887-7901.
53. Dahlberg, J.E. and Lund, E. 2004. Does protein synthesis occur in the nucleus? Curr. Opin. Cell Biol. 16: 335-338.
54. Danckwardt, S., Neu-Yilik, G., Thermann, R., Frede, U., Hentze, M.W., and Kulozik, A.E. 2002. Abnormally spliced -globin mRNAs: A single point mutation generates transcripts sensitive and insensitive to nonsense-mediated mRNA decay. Blood 99: 1811-1816.
55. Das, B., Guo, Z., Russo, P., Chartrand, P., and Sherman, F. 2000. The role of nuclear cap binding protein Cbc1p of yeast in mRNA termination and degradation. Mol. Cell. Biol. 20: 2827-2838.
56. Degot, S., Le Hir, H., Alpy, F., Kedinger, V., Stoll, I., Wendling, C., Seraphin, B., Rio, M.C., and Tomasetto, C. 2004. Association of the breast cancer protein MLN51 with the exon junction complex via its speckle localizer and RNA binding module. J. Biol. Chem. 279: 33702-33715.
57. Denning, G., Jamieson, L., Maquat, L.E., Thompson, E.A., and Fields, A.P. 2001. Cloning of a novel phosphatidylinositol kinase-related kinase: Characterization of the human SMG-1 RNA surveillance protein. J. Biol. Chem. 276: 22709-22714.
58. Dickey, L.F., Nguyen, T.T., Allen, G.C., and Thompson, W.F. 1994. Light modulation of ferredoxin mRNA abundance requires an open reading frame. Plant Cell 6: 1171-1176.
59. Dimaano, C. and Ullman, K.S. 2004. Nucleocytoplasmic transport: Integrating mRNA production and turnover with export through the nuclear pore. Mol. Cell. Biol. 24: 3069-3076.
60. Doma, M.K. and Parker, R. 2006. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440: 561-564.
61. Dostie, J. and Dreyfuss, G. 2002. Translation is required to remove Y14 from mRNAs in the cytoplasm. Curr. Biol. 12: 1060-1067.
62. Dreyfuss, G., Kim, N.V., and Kataoka, N. 2002. Messenger-RNA-binding proteins and the messages they carry. Nat. Rev. Mol. Cell Biol. 3: 195-205.
63. Durand, S., Cougot, N., Mahuteau-Betzer, F., Nugyen, C.H., Grieson, D.L., Bertrand, E., Tazi, J., and Lejeune, F. 2007. Inhibition of nonsense-mediated mRNA decay (NMD) by a new chemical molecule reveals the dynamic of NMD factors in P-bodies. J. Cell Biol. (in press).
64. Edwalds-Gilbert, G., Veraldi, K.L., and Milcarek, C. 1997. Alternative poly(A) site selection in complex transcription units: Means to an end? Nucleic Acids Res. 25: 2547-2561.
65. Fasken, M.B. and Corbett, A.H. 2005. Process or perish: Quality control in mRNA biogenesis. Nat. Struct. Mol. Biol. 12: 482-488.
66. Ferraiuolo, M.A., Lee, C.S., Ler, L.W., Hsu, J.L., Costa-Mattioli, M., Luo, M.J., Reed, R., and Sonenberg, N. 2004. A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay. Proc. Natl. Acad. Sci. 101: 4118-4123.
67. Frischmeyer, P.A., van Hoof, A., O'Donnell, K., Guerrerio, A.L., Parker, R., and Dietz, H.C. 2002. An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295: 2258-2261.
68. Fukuhara, N., Ebert, J., Unterholzner, L., Lindner, D., Izaurralde, E., and Conti, E. 2005. SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway. Mol. Cell 17: 537-547.
69. Gao, Q., Das, B., Sherman, F., and Maquat, L.E. 2005. Cap-binding protein 1-mediated and eukaryotic translation initiation factor 4E-mediated pioneer rounds of translation in yeast. Proc. Natl. Acad. Sci. 102: 4258-4263.
70. Gatfield, D. and Izaurralde, E. 2004. Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila. Nature 429: 575-578.
71. Gatfield, D., Unterholzner, L., Ciccarelli, F.D., Bork, P., and Izaurralde, E. 2003. Nonsense-mediated mRNA decay in Drosophila: At the intersection of the yeast and mammalian pathways. EMBO J. 22: 3960-3970.
72. Gehring, N.H., Neu-Yilik, G., Schell, T., Hentze, M.W., and Kulozik, A.E. 2003. Y14 and hUpf3b form an NMD-activating complex. Mol. Cell 11: 939-949.
73. Gehring, N.H., Kunz, J.B., Neu-Yilik, G., Breit, S., Viegas, M.H., Hentze, M.W., and Kulozik, A.E. 2005. Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. Mol. Cell 20: 65-75.
74. Gersappe, A. and Pintel, D.J. 1999. A premature termination codon interferes with the nuclear function of an exon splicing enhancer in an open reading frame-dependent manner. Mol. Cell. Biol. 19: 1640-1650.
75. Gingras, A.C., Raught, B., and Sonenberg, N. 1999. eIF4 initiation factors: Effectors of mRNA recruitment to ribosomes and regulators of translation. Annu. Rev. Biochem. 68: 913-963.
76. Giorgi, C. and Moore, M.J. 2007. The nuclear nurture and cytoplasmic nature of localized mRNPs. Semin. Cell Dev. Biol. 18: 186-193.
77. Gonzalez, C.I., Ruiz-Echevarría, M.J., Vasudevan, S., Henry, M.F., and Peltz, S.W. 2000. The yeast hnRNP-like protein Hrp1/Nab4 marks a transcript for nonsense-mediated mRNA decay. Mol. Cell 5: 489-499.
78. Gonzalez, C.I., Bhattacharya, A., Wang, W., and Peltz, S.W. 2001. Nonsense-mediated mRNA decay in Saccharomyces cerevisiae. Gene 274: 15-25.
79. Graber, J.H., Cantor, C.R., Mohr, S.C., and Smith, T.F. 1999. Genomic detection of new yeast pre-mRNA 3′-end-processing signals. Nucleic Acids Res. 27: 888-894.
80. Gray, N.K., Coller, J.M., Dickson, K.S., and Wickens, M. 2000. Multiple portions of poly(A)-binding protein stimulate translation in vivo. EMBO J. 19: 4723-4733.
81. Grimson, A., O'Connor, S., Newman, C.L., and Anderson, P. 2004. SMG-1 is a phosphatidylinositol kinase-related protein kinase required for nonsense-mediated mRNA decay in Caenorhabditis elegans. Mol. Cell. Biol. 24: 7483-7490.
82. Guan, Q., Zheng, W., Tang, S., Liu, X., Zinkel, R.A., Tsui, K.W., Yandell, B.S., and Culbertson, M.R. 2006. Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genet. 2: e203. doi: 10.1371/journal.pgen.0020203.
83. Gudikote, J.P. and Wilkinson, M.F. 2002. T-cell receptor sequences that elicit strong down-regulation of premature termination codon-bearing transcripts. EMBO J. 21: 125-134.
84. Gudikote, J.P., Imam, J.S., Garcia, R.F., and Wilkinson, M.F. 2005. RNA splicing promotes translation and RNA surveillance. Nat. Struct. Mol. Biol. 12: 801-809.
85. Hayes, C.S. and Sauer, R.T. 2003. Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol. Cell 12: 903-911.
86. He, F. and Jacobson, A. 1995. Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen. Genes & Dev. 9: 437-454.
87. He, F. and Jacobson, A. 2001. Upf1p, Nmd2p, and Upf3p regulate the decapping and exonucleolytic degradation of both nonsense-containing mRNAs and wild-type mRNAs. Mol. Cell. Biol. 21: 1515-1530.
88. He, F., Li, X., Spatrick, P., Casillo, R., Dong, S., and Jacobson, A. 2003. Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast. Mol. Cell 12: 1439-1452.
89. Hirose, T., Shu, M.D., and Steitz, J.A. 2004. Splicing of U12-type introns deposits an exon junction complex competent to induce nonsense-mediated mRNA decay. Proc. Natl. Acad. Sci. 101: 17976-17981.
90. Hodgkin, J., Papp, A., Pulak, R., Ambros, V., and Anderson, P. 1989. A new kind of informational suppression in the nematode Caenorhabditis elegans. Genetics 123: 301-313.
91. Holbrook, J.A., Neu-Yilik, G., Hentze, M.W., and Kulozik, A.E. 2004. Nonsense-mediated decay approaches the clinic. Nat. Genet. 36: 801-808.
92. Holbrook, J.A., Neu-Yilik, G., Gehring, N.H., Kulozik, A.E., and Hentze, M.W. 2006. Internal ribosome entry sequence-mediated translation initiation triggers nonsense-mediated decay. EMBO Rep. 7: 722-726.
93. Hong, X., Scofield, D.G., and Lynch, M. 2006. Intron size, abundance, and distribution within untranslated regions of genes. Mol. Biol. Evol. 23: 2392-2404.
94. Hosoda, N., Kim, Y.K., Lejeune, F., and Maquat, L.E. 2005. CBP80 promotes interaction of Upf1 with Upf2 during nonsense-mediated mRNA decay in mammalian cells. Nat. Struct. Mol. Biol. 12: 893-901.
95. Hosoda, N., Lejeune, F., and Maquat, L.E. 2006. Evidence that poly(A) binding protein C1 binds nuclear pre-mRNA poly(A) tails. Mol. Cell. Biol. 26: 3085-3097.
96. Houseley, J., LaCava, J., and Tollervey, D. 2006. RNA-quality control by the exosome. Nat. Rev. Mol. Cell Biol. 7: 529-539.
97. Iborra, F.J., Jackson, D.A., and Cook, P.R. 2004. The case for nuclear translation. J. Cell Sci. 117: 5713-5720.
98. Inada, T. and Aiba, H. 2005. Translation of aberrant mRNAs lacking a termination codon or with a shortened 3′-UTR is repressed after initiation in yeast. EMBO J. 24: 1584-1595.
99. Ishigaki, Y., Li, X., Serin, G., and Maquat, L.E. 2001. Evidence for a pioneer round of mRNA translation: mRNAs subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20. Cell 106: 607-617.
100. Isshiki, M., Yamamoto, Y., Satoh, H., and Shimamoto, K. 2001. Nonsense-mediated decay of mutant waxy mRNA in rice. Plant Physiol. 125: 1388-1395.
101. Ito-Harashima, S., Kuroha, K., Tatematsu, T., and Inada, T. 2007. Translation of the poly(A) tail plays crucial roles in nonstop mRNA surveillance via translation repression and protein destabilization by proteasome in yeast. Genes & Dev. 21: 519-524.
102. Izaurralde, E., Lewis, J., McGuigan, C., Jankowska, M., Darzynkiewicz, E., and Mattaj, I.W. 1994. A nuclear cap binding protein complex involved in pre-mRNA splicing. Cell 78: 657-668.
103. Jumaa, H. and Nielsen, P.J. 1997. The splicing factor SRp20 modifies splicing of its own mRNA and ASF/SF2 antagonizes this regulation. EMBO J. 16: 5077-5085.
104. Kadlec, J., Izaurralde, E., and Cusack, S. 2004. The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3. Nat. Struct. Mol. Biol. 11: 330-337.
105. Kadlec, J., Guilligay, D., Ravelli, R.B., and Cusack, S. 2006. Crystal structure of the UPF2-interacting domain of nonsense-mediated mRNA decay factor UPF1. RNA 12: 1817-1824.
106. Kahvejian, A., Svitkin, Y.V., Sukarieh, R., M'Boutchou, M.N., and Sonenberg, N. 2005. Mammalian poly(A)-binding protein is a eukaryotic translation initiation factor, which acts via multiple mechanisms. Genes & Dev. 19: 104-113.
107. Karim, M.M., Svitkin, Y.V., Kahvejian, A., De Crescenzo, G., Costa-Mattioli, M., and Sonenberg, N. 2006. A mechanism of translational repression by competition of Paip2 with eIF4G for poly(A) binding protein (PABP) binding. Proc. Natl. Acad. Sci. 103: 9494-9499.
108. Kashima, I., Yamashita, A., Izumi, N., Kataoka, N., Morishita, R., Hoshino, S., Ohno, M., Dreyfuss, G., and 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 & Dev. 20: 355-367.
109. Katahira, J., Strasser, K., Podtelejnikov, A., Mann, M., Jung, J.U., and Hurt, E. 1999. The Mex67p-mediated nuclear mRNA export pathway is conserved from yeast to human. EMBO J. 18: 2593-2609.
110. Kataoka, N., Yong, J., Kim, V.N., Velazquez, F., Perkinson, R.A., Wang, F., and Dreyfuss, G. 2000. Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm. Mol. Cell 6: 673-682.
111. Kaygun, H. and Marzluff, W.F. 2005. Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1. Nat. Struct. Mol. Biol. 12: 794-800.
112. Keeling, K.M., Lanier, J., Du, M., Salas-Marco, J., Gao, L., Kaenjak-Angeletti, A., and Bedwell, D.M. 2004. Leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S. cerevisiae. RNA 10: 691-703.
113. Kennedy, S., Wang, D., and Ruvkun, G. 2004. A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature 427: 645-649.
114. Kertesz, S., Kerenyi, Z., Merai, Z., Bartos, I., Palfy, T., Barta, E., and Silhavy, D. 2006. Both introns and long 3′-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants. Nucleic Acids Res. 34: 6147-6157.
115. Khaleghpour, K., Svitkin, Y.V., Craig, A.W., DeMaria, C.T., Deo, R.C., Burley, S.K., and Sonenberg, N. 2001. Translational repression by a novel partner of human poly(A) binding protein, Paip2. Mol. Cell 7: 205-216.
116. Kim, E., Ambroziak, P., Veniant, M.M., Hamilton, R.L., and Young, S.G. 1998. A gene-targeted mouse model for familial hypobetalipoproteinemia. Low levels of apolipoprotein B mRNA in association with a nonsense mutation in exon 26 of the apolipoprotein B gene. J. Biol. Chem. 273: 33977-33984.
117. Kim, V.N., Kataoka, N., and Dreyfuss, G. 2001a. Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex. Science 293: 1832-1836.
118. Kim, V.N., Yong, J., Kataoka, N., Abel, L., Diem, M.D., and Dreyfuss, G. 2001b. The Y14 protein communicates to the cytoplasm the position of exon-exon junctions. EMBO J. 20: 2062-2068.
119. Kim, Y.K., Furic, L., Desgroseillers, L., and Maquat, L.E. 2005. Mammalian Staufen1 recruits Upf1 to specific mRNA 3′UTRs so as to elicit mRNA decay. Cell 120: 195-208.
120. Kim, Y.K., Furic, L., Parisien, M., Major, F., DesGroseillers, L., and Maquat, L.E. 2007. Staufen1 regulates diverse classes of mammalian transcripts. EMBO J. 26: 2670-2681.
121. Kloc, M. and Etkin, L.D. 2005. 2005. RNA localization mechanisms in oocytes. J. Cell Sci. 118: 269-282.
122. Kunz, J.B., Neu-Yilik, G., Hentze, M.W., Kulozik, A.E., and Gehring, N.H. 2006. Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation. RNA 12: 1015-1022.
123. Kuzmiak, H.A. and Maquat, L.E. 2006. Applying nonsense-mediated mRNA decay research to the clinic: Progress and challenges. Trends Mol. Med. 12: 306-316.
124. Lareau, L.F., Green, R.E., Bhatnagar, R.S., and Brenner, S.E. 2004. The evolving roles of alternative splicing. Curr. Opin. Struct. Biol. 14: 273-282.
125. Lareau, L.F., Inada, M., Green, R.E., Wengrod, J.C., and Brenner, S.E. 2007. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446: 926-929.
126. Lasko, P., Cho, P., Poulin, F., and Sonenberg, N. 2005. Contrasting mechanisms of regulating translation of specific Drosophila germline mRNAs at the level of 5′ cap structure binding. Biochem. Soc. Trans. 33: 1544-1546.
127. Le Hir, H., Izaurralde, E., Maquat, L.E., and Moore, M.J. 2000. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 19: 6860-6869.
128. Le Hir, H., Gatfield, D., Braun, I.C., Forler, D., and Izaurralde, E. 2001a. The protein Mago provides a link between splicing and mRNA localization. EMBO Rep. 2: 1119-1124.
129. Le Hir, H., Gatfield, D., Izaurralde, E., and Moore, M.J. 2001b. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 20: 4987-4997.
130. Le Hir, H., Nott, A., and Moore, M.J. 2003. How introns influence and enhance eukaryotic gene expression. Trends Biochem. Sci. 28: 215-220.
131. Leeds, P., Peltz, S.W., Jacobson, A., and Culbertson, M.R. 1991. The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes & Dev. 5: 2303-2314.
132. Lehner, B. and Sanderson, C.M. 2004. A protein interaction framework for human mRNA degradation. Genome Res. 14: 1315-1323.
133. Lejeune, F. and Maquat, L.E. 2005. Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr. Opin. Cell Biol. 17: 309-315.
134. Lejeune, F., Ishigaki, Y., Li, X., and Maquat, L.E. 2002. The exon junction complex is detected on CBP80-bound but not eIF4E-bound mRNA in mammalian cells: Dynamics of mRNP remodeling. EMBO J. 21: 3536-3545.
135. Lejeune, F., Li, X., and Maquat, L.E. 2003. Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. Mol. Cell 12: 675-687.
136. Lejeune, F., Ranganathan, A.C., and Maquat, L.E. 2004. eIF4G is required for the pioneer round of translation in mammalian cells. Nat. Struct. Mol. Biol. 11: 992-1000.
137. Lelivelt, M.J. and Culbertson, M.R. 1999. Yeast Upf proteins required for RNA surveillance affect global expression of the yeast transcriptome. Mol. Cell. Biol. 19: 6710-6719.
138. Lewis, B.P., Green, R.E., and Brenner, S.E. 2003. Evidence for the widespread coupling of alternative splicing and nonsensemediated mRNA decay in humans. Proc. Natl. Acad. Sci. 100: 189-192.
139. Li, S. and Wilkinson, M.F. 1998. Nonsense surveillance in lymphocytes? Immunity 8: 135-141.
140. Li, B., Wachtel, C., Miriami, E., Yahalom, G., Friedlander, G., Sharon, G., Sperling, R., and Sperling, J. 2002. Stop codons affect 5′ splice site selection by surveillance of splicing. Proc. Natl. Acad. Sci. 99: 5277-5282.
141. Lim, S.K. and Maquat, L.E. 1992. Human β-globin mRNAs that harbor a nonsense codon are degraded in murine erythroid tissues to intermediates lacking regions of exon I or exons I and II that have a cap-like structure at the 5′ termini. EMBO J. 11: 3271-3278.
142. Lim, S.K., Mullins, J.J., Chen, C.M., Gross, K.W., and Maquat, L.E. 1989. Novel metabolism of several β zero-thalassemic β-globin mRNAs in the erythroid tissues of transgenic mice. EMBO J. 8: 2613-2619.
143. Lim, S.K., Sigmund, C.D., Gross, K.W., and Maquat, L.E. 1992. Nonsense codons in human β-globin mRNA result in the production of mRNA degradation products. Mol. Cell. Biol. 12: 1149-1161.
144. Longman, D., Plasterk, R.H., Johnstone, I.L., and Caceres, J.F. 2007. Mechanistic insights and identification of two novel factors in the C. elegans NMD pathway. Genes & Dev. 21: 1075-1085.
145. Lloyd, R.E. 2006. Translational control by viral proteinases. Virus Res. 119: 76-88.
146. Luo, M.J. and Reed, R. 1999. Splicing is required for rapid and efficient mRNA export in metazoans. Proc. Natl. Acad. Sci. 96: 14937-14942.
147. Lykke-Andersen, J. 2002. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol. Cell. Biol. 22: 8114-8121.
148. Lykke-Andersen, J., Shu, M.D., and Steitz, J.A. 2000. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. Cell 103: 1121-1131.
149. Lykke-Andersen, J., Shu, M.D., and Steitz, J.A. 2001. Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1. Science 293: 1836-1839.
150. Lynch, M., Hong, X., and Scofield, D.G. 2006. NMD and the evolution of eukaryotic gene structure. In Nonsense-mediated mRNA decay. (ed. L.E. Maquat). pp 197-211. Molecular biology intelligence unit. Landes Bioscience, Georgetown, TX.
151. Lytle, J.R. and Steitz, J.A. 2004. Premature termination codons do not affect the rate of splicing of neighboring introns. RNA 10: 657-668.
152. Maderazo, A.B., Belk, J.P., He, F., and Jacobson, A. 2003. Nonsense-containing mRNAs that accumulate in the absence of a functional nonsense-mediated mRNA decay pathway are destabilized rapidly upon its restitution. Mol. Cell. Biol. 23: 842-851.
153. Maquat, L.E. 2002. Molecular biology. Skiing toward nonstop mRNA decay. Science 295: 2221-2222.
154. Maquat, L.E. 2004a. Nonsense-mediated mRNA decay: Splicing, translation and mRNP dynamics. Nat. Rev. Mol. Cell Biol. 5: 89-99.
155. Maquat, L.E. 2004b. Nonsense-mediated mRNA decay: A comparative analysis of different species. Curr. Genomics 5: 175-190.
156. Maquat, L.E. 2005. Nonsense-mediated mRNA decay in mammals. J. Cell Sci. 118: 1773-1776.
157. Maquat, L.E., ed. 2006. Nonsense-mediated mRNA decay. Molecular biology intelligence unit. Landes Bioscience, Georgetown, TX.
158. Mayeda, A., Badolato, J., Kobayashi, R., Zhang, M.Q., Gardiner, E.M., and Krainer, A.R. 1999. Purification and characterization of human RNPS1: A general activator of pre-mRNA splicing. EMBO J. 18: 4560-4570.
159. McPherson, J.D., Marra, M., Hillier, L., Waterston, R.H., Chinwalla, A., Wallis, J., Sekhon, M., Wylie, K., Mardis, E.R., Wilson, R.K., et al. 2001. A physical map of the human genome. Nature 409: 934-941.
160. Meaux, S. and Van Hoof, A. 2006. Yeast transcripts cleaved by an internal ribozyme provide new insight into the role of the cap and poly(A) tail in translation and mRNA decay. RNA 12: 1323-1337.
161. Mendell, J.T., Medghalchi, S.M., Lake, R.G., Noensie, E.N., and Dietz, H.C. 2000. Novel Upf2p orthologues suggest a functional link between translation initiation and nonsense surveillance complexes. Mol. Cell. Biol. 20: 8944-8957.
162. Mendell, J.T., ap Rhys, C.M., and Dietz, H.C. 2002. Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts. Science 298: 419-422.
163. Mendell, J.T., Sharifi, N.A., Meyers, J.L., Martinez-Murillo, F., and Dietz, H.C. 2004. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36: 1073-1078.
164. Metzstein, M.M. and Krasnow, M.A. 2006. Functions of the nonsense-mediated mRNA decay pathway in Drosophila development. PLoS Genet. 2: e180. doi: 10.1371/journal.pgen.0020180.
165. Meyer, S., Temme, C., and Wahle, E. 2004. Messenger RNA turnover in eukaryotes: Pathways and enzymes. Crit. Rev. Biochem. Mol. Biol. 39: 197-216.
166. Miriami, E., Sperling, R., Sperling, J., and Motro, U. 2004. Regulation of splicing: The importance of being translatable. RNA 10: 1-4.
167. Mitchell, P. and Tollervey, D. 2003. An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3′ → 5′ degradation. Mol. Cell 11: 1405-1413.
168. Mitrovich, Q.M. and Anderson, P. 2000. Unproductively spliced ribosomal protein mRNAs are natural targets of mRNA surveillance in C. elegans. Genes & Dev. 14: 2173-2184.
169. Moore, M.J. 2005. From birth to death: The complex lives of eukaryotic mRNAs. Science 309: 1514-1518.
170. Moriarty, P.M., Reddy, C.C., and Maquat, L.E. 1998. Selenium deficiency reduces the abundance of mRNA for Se-dependent glutathione peroxidase 1 by a UGA-dependent mechanism likely to be nonsense codon-mediated decay of cytoplasmic mRNA. Mol. Cell. Biol. 18: 2932-2939.
171. Mouse Genome Sequencing Consortium 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
172. Muhlrad, D. and Parker, R. 1994. Premature translational termination triggers mRNA decapping. Nature 370: 578-581.
173. Muhlrad, D. and Parker, R. 1999. Recognition of yeast mRNAs as 'nonsense containing' leads to both inhibition of mRNA translation and mRNA degradation: Implications for the control of mRNA decapping. Mol. Biol. Cell 10: 3971-3978.
174. Nagy, E. and Maquat, L.E. 1998. A rule for termination-codon position within intron-containing genes: When nonsense affects RNA abundance. Trends Biochem. Sci. 23: 198-199.
175. Neu-Yilik, G., Gehring, N.H., Thermann, R., Frede, U., Hentze, M.W., and Kulozik, A.E. 2001. Splicing and 3′ end formation in the definition of nonsense-mediated decay-competent human β-globin mRNPs. EMBO J. 20: 532-540.
176. Neu-Yilik, G., Gehring, N.H., Hentze, M.W., and Kulozik, A.E. 2004. Nonsense-mediated mRNA decay: From vacuum cleaner to Swiss army knife. Genome Biol. 5: 218.
177. Ni, J.Z., Grate, L., Donohue, J.P., Preston, C., Nobida, N., O'Brien, G., Shiue, L., Clark, T.A., Blume, J.E., and Ares Jr., M. 2007. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes & Dev. 21: 708-718.
178. Noble, C.G. and Song, H. 2007. MLN51 stimulates the RNA-helicase activity of eIF4AIII. PLoS ONE 2: e303. doi: 10.1371/journal.pone.0000303.
179. Ohnishi, T., Yamashita, A., Kashima, I., Schell, T., Anders, K.R., Grimson, A., Hachiya, T., Hentze, M.W., Anderson, P., and Ohno, S. 2003. Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. Mol. Cell 12: 1187-1200.
180. Onouchi, H., Nagami, Y., Haraguchi, Y., Nakamoto, M., Nishimura, Y., Sakurai, R., Nagao, N., Kawasaki, D., Kadokura, Y., and Naito, S. 2005. Nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in the CGS1 gene of Arabidopsis. Genes & Dev. 19: 1799-1810.
181. Ougland, R., Zhang, C.M., Liiv, A., Johansen, R.F., Seeberg, E., Hou, Y.M., Remme, J., and Falnes, P.O. 2004. AlkB restores the biological function of mRNA and tRNA inactivated by chemical methylation. Mol. Cell 16: 107-116.
182. Page, M.F., Carr, B., Anders, K.R., Grimson, A., and Anderson, P. 1999. SMG-2 is a phosphorylated protein required for mRNA surveillance in Caenorhabditis elegans and related to Upf1p of yeast. Mol. Cell. Biol. 19: 5943-5951.
183. Pal, M., Ishigaki, Y., Nagy, E., and 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: 5-15.
184. Palacios, I.M., Gatfield, D., St Johnston, D., and Izaurralde, E. 2004. An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay. Nature 427: 753-757.
185. Pan, Q., Saltzman, A.L., Kim, Y.K., Misquitta, C., Shai, O., Maquat, L.E., Frey, B.J., and Blencowe, B.J. 2006. Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes & Dev. 20: 153-158.
186. Park, N.I. and Muench, D.G. 2007. Biochemical and cellular characterization of the plant ortholog of PYM, a protein that interacts with the exon junction complex core proteins Mago and Y14. Planta 225: 625-639.
187. Parker, R. and Sheth, U. 2007. P bodies and the control of mRNA translation and degradation. Mol. Cell 25: 635-646.
188. Parker, R. and Song, H. 2004. The enzymes and control of eukaryotic mRNA turnover. Nat. Struct. Mol. Biol. 11: 121-127.
189. Petracek, M.E., Nuygen, T., Thompson, W.F., and Dickey, L.F. 2000. Premature termination codons destabilize ferredoxin-1 mRNA when ferredoxin-1 is translated. Plant J. 21: 563-569.
190. Plant, E.P., Wang, P., Jacobs, J.L., and Dinman, J.D. 2004. A programmed-1 ribosomal frameshift signal can function as a cis-acting mRNA destabilizing element. Nucleic Acids Res. 32: 784-790.
191. Pulak, R. and Anderson, P. 1993. mRNA surveillance by the Caenorhabditis elegans smg genes. Genes & Dev. 7: 1885-1897.
192. Rajavel, K.S. and Neufeld, E.F. 2001. Nonsense-mediated mRNA decay of human HexA mRNA. Mol. Cell. Biol. 21: 5512-5519.
193. Reed, R. 2003. Coupling transcription, splicing and mRNA export. Curr. Opin. Cell Biol. 15: 326-331.
194. Reed, R. and Cheng, H. 2005. TREX, SR proteins and export of mRNA. Curr. Opin. Cell Biol. 17: 269-273.
195. Rehwinkel, J., Letunic, I., Raes, J., Bork, P., and Izaurralde, E. 2005. Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA 11: 1530-1544.
196. Rehwinkel, J., Raes, J., and Izaurralde, E. 2006. Nonsense-mediated mRNA decay: Target genes and functional diversification of effectors. Trends Biochem. Sci. 31: 639-646.
197. Rodrigues, J.P., Rode, M., Gatfield, D., Blencowe, B.J., Carmo-Fonseca, M., and Izaurralde, E. 2001. REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus. Proc. Natl. Acad. Sci. 98: 1030-1035.
198. Romao, L., Inacio, A., Santos, S., Avila, M., Faustino, P., Pacheco, P., and Lavinha, J. 2000. Nonsense mutations in the human β-globin gene lead to unexpected levels of cytoplasmic mRNA accumulation. Blood 96: 2895-2901.
199. Rose, A.B. 2004. The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis. Plant J. 40: 744-751.
200. Roy, S.W. and Gilbert, W. 2006. The evolution of spliceosomal introns: Patterns, puzzles and progress. Nat. Rev. Genet. 7: 211-221.
201. Ruiz-Echevarría, M.J. and Peltz, S.W. 2000. The RNA binding protein Pub1 modulates the stability of transcripts containing upstream open reading frames. Cell 101: 741-751.
202. Saguez, C., Olesen, J.R., and Jensen, T.H. 2005. Formation of export-competent mRNP: Escaping nuclear destruction. Curr. Opin. Cell Biol. 17: 287-293.
203. Schwartz, A.M., Komarova, T.V., Skulachev, M.V., Zvereva, A.S., Dorokhov, Y.L., and Atabekov, J.G. 2006. Stability of plant mRNAs depends on the length of the 3′-untranslated region. Biochemistry (Mosc.) 71: 1377-1384.
204. Scofield, D.G., Hong, X., and Lynch, M. 2007. Position of the final intron in full-length transcripts: Determined by NMD? Mol. Biol. Evol. 24: 896-899.
205. Serin, G., Gersappe, A., Black, J.D., Aronoff, R., and Maquat, L.E. 2001. Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4). Mol. Cell. Biol. 21: 209-223.
206. Shen, B. and Goodman, H.M. 2004. Uridine addition after microRNA-directed cleavage. Science 306: 997.
207. Sheth, U. and Parker, R. 2006. Targeting of aberrant mRNAs to cytoplasmic processing bodies. Cell 125: 1095-1109.
208. Shibuya, T., Tange, T.O., Sonenberg, N., and Moore, M.J. 2004. eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat. Struct. Mol. Biol. 11: 346-351.
209. Shibuya, T., Tange, T.O., Stroupe, M.E., and Moore, M.J. 2006. Mutational analysis of human eIF4AIII identifies regions necessary for exon junction complex formation and nonsense-mediated mRNA decay. RNA 12: 360-374.
210. Silva, A.L., Pereira, F.J., Morgado, A., Kong, J., Martins, R., Faustino, P., Liebhaber, S.A., and Romao, L. 2006. The canonical UPF1-dependent nonsense-mediated mRNA decay is inhibited in transcripts carrying a short open reading frame independent of sequence context. RNA 12: 2160-2170.
211. Sparks, K.A. and Dieckmann, C.L. 1998. Regulation of poly(A) site choice of several yeast mRNAs. Nucleic Acids Res. 26: 4676-4687.
212. Stalder, L. and Mühlemann, O. 2007. Transcriptional silencing of nonsense codon-containing immunoglobulin mu genes requires translation of its mRNA. J. Biol. Chem. 282: 16079-16085.
213. Stevens, A., Wang, Y., Bremer, K., Zhang, J., Hoepfner, R., Antoniou, M., Schoenberg, D.R., and Maquat, L.E. 2002. β-Globin mRNA decay in erythroid cells: UG site-preferred endonucleolytic cleavage that is augmented by a premature termination codon. Proc. Natl. Acad. Sci. 99: 12741-12746.
214. St Johnston, D. 2005. Moving messages: The intracellular localization of mRNAs. Nat. Rev. Mol. Cell Biol. 6: 363-375.
215. Stoilov, P., Daoud, R., Nayler, O., and Stamm, S. 2004. Human tra2-β1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA. Hum. Mol. Genet. 13: 509-524.
216. Stroupe, M.E., Tange, T.O., Thomas, D.R., Moore, M.J., and Grigorieff, N. 2006. The three-dimensional arcitecture of the EJC core. J. Mol. Biol. 360: 743-749.
217. Stutz, F., Bachi, A., Doerks, T., Braun, I.C., Seraphin, B., Wilm, M., Bork, P., and Izaurralde, E. 2000. REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. RNA 6: 638-650.
218. Sun, X., Moriarty, P.M., and Maquat, L.E. 2000. Nonsense-mediated decay of glutathione peroxidase 1 mRNA in the cytoplasm depends on intron position. EMBO J. 19: 4734-4744.
219. Sun, X., Li, X., Moriarty, P.M., Henics, T., LaDuca, J.P., and Maquat, L.E. 2001. Nonsense-mediated decay of mRNA for the selenoprotein phospholipid hydroperoxide glutathione peroxidase is detectable in cultured cells but masked or inhibited in rat tissues. Mol. Biol. Cell 12: 1009-1017.
220. Sunohara, T., Jojima, K., Yamamoto, Y., Inada, T., and Aiba, H. 2004. Nascent-peptide-mediated ribosome stalling at a stop codon induces mRNA cleavage resulting in nonstop mRNA that is recognized by tmRNA. RNA 10: 378-386.
221. Sureau, A., Gattoni, R., Dooghe, Y., Stevenin, J., and Soret, J. 2001. SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs. EMBO J. 20: 1785-1796.
222. Tange, T.O., Shibuya, T., Jurica, M.S., and Moore, M.J. 2005. Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. RNA 11: 1869-1883.
223. Tarun Jr., S.Z. and Sachs, A.B. 1996. Association of the yeast poly(A) tail binding protein with translation initiation factor eIF-4G. EMBO J. 15: 7168-7177.
224. Templeton, G.W. and Moorhead, G.B. 2005. The phosphoinositide-3-OH- kinase-related kinases of Arabidopsis thaliana. EMBO Rep. 6: 723-728.
225. Thermann, R., Neu-Yilik, G., Deters, A., Frede, U., Wehr, K., Hagemeier, C., Hentze, M.W., and Kulozik, A.E. 1998. Binary specification of nonsense codons by splicing and cytoplasmic translation. EMBO J. 17: 3484-3494.
226. Tollervey, D. 2006. Molecular biology: RNA lost in translation. Nature 440: 425-426.
227. Uchida, N., Hoshino, S., Imataka, H., Sonenberg, N., and Katada, T. 2002. A novel role of the mammalian GSPT/eRF3 associating with poly(A)-binding protein in Cap/Poly(A)-dependent translation. J. Biol. Chem. 277: 50286-50292.
228. Unterholzner, L. and Izaurralde, E. 2004. SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. Mol. Cell 16: 587-596.
229. Urlaub, G., Mitchell, P.J., Ciudad, C.J., and Chasin, L.A. 1989. Nonsense mutations in the dihydrofolate reductase gene affect RNA processing. Mol. Cell. Biol. 9: 2868-2880.
230. van Hoof, A. 2005. Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication. Genetics 171: 1455-1461.
231. van Hoof, A. and Green, P.J. 1996. Premature nonsense codons decrease the stability of phytohemagglutinin mRNA in a position-dependent manner. Plant J. 10: 415-424.
232. van Hoof, A., Frischmeyer, P.A., Dietz, H.C., and Parker, R. 2002. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295: 2262-2264.
233. Vasudevan, S., Peltz, S.W., and Wilusz, C.J. 2002. Non-stop decay - A new mRNA surveillance pathway. Bioessays 24: 785-788.
234. Venter, J.C., Adams, M.D., Meyers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
235. Vinciguerra, P. and Stutz, F. 2004. mRNA export: An assembly line from genes to nuclear pores. Curr. Opin. Cell Biol. 16: 285-292.
236. Voelker, T.A., Moreno, J., and Chrispeels, M.J. 1990. Expression analysis of a pseudogene in transgenic tobacco: A frameshift mutation prevents mRNA accumulation. Plant Cell 2: 255-261.
237. Wachtel, C., Li, B., Sperling, J., and Sperling, R. 2004. Stop codon-mediated suppression of splicing is a novel nuclear scanning mechanism not affected by elements of protein synthesis and NMD. RNA 10: 1740-1750.
238. Wagner, E. and Lykke-Andersen, J. 2002. mRNA surveillance: The perfect persist. J. Cell Sci. 115: 3033-3038.
239. Wang, W., Czaplinski, K., Rao, Y., and Peltz, S.W. 2001. The role of Upf proteins in modulating the translation read-through of nonsense-containing transcripts. EMBO J. 20: 880-890.
240. Wang, J., Chang, Y.F., Hamilton, J.I., and Wilkinson, M.F. 2002a. Nonsense-associated altered splicing: A frame-dependent response distinct from nonsense-mediated decay. Mol. Cell 10: 951-957.
241. Wang, J., Gudikote, J.P., Olivas, O.R., and Wilkinson, M.F. 2002b. Boundary-independent polar nonsense-mediated decay. EMBO Rep. 3: 274-279.
242. Wang, J., Hamilton, J.I., Carter, M.S., Li, S., and Wilkinson, M.F. 2002c. Alternatively spliced TCR mRNA induced by disruption of reading frame. Science 297: 108-110.
243. Wang, W., Cajigas, I.J., Peltz, S.W., Wilkinson, M.F., and Gonzalez, C.I. 2006. Role for Upf2p phosphorylation in Saccharomyces cerevisiae nonsense-mediated mRNA decay. Mol. Cell. Biol. 26: 3390-3400.
244. Weil, J.E. and Beemon, K.L. 2006. A 3′ UTR sequence stabilizes termination codons in the unspliced RNA of Rous sarcoma virus. RNA 12: 102-110.
245. Weischenfeldt, J., Lykke-Andersen, J., and Porse, B. 2005. Messenger RNA surveillance: Neutralizing natural nonsense. Curr. Biol. 15: R559-R562. doi: 10.1016/j.cub.2005.07.002.
246. Weng, Y., Czaplinski, K., and Peltz, S.W. 1996. Identification and characterization of mutations in the UPF1 gene that affect nonsense suppression and the formation of the Upf protein complex but not mRNA turnover. Mol. Cell. Biol. 16: 5491-5506.
247. Wittmann, J., Hol, E.M., and Jäck, H.M. 2006. hUPF2 silencing identifies physiologic substrates of mammalian nonsensemediated mRNA decay. Mol. Cell. Biol. 26: 1272-1287.
248. Wollerton, M.C., Gooding, C., Wagner, E.J., Garcia-Blanco, M.A., and Smith, C.W. 2004. Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol. Cell 13: 91-100.
249. Yamashita, A., Ohnishi, T., Kashima, I., Taya, Y., and Ohno, S. 2001. Human SMG-1, a novel phosphatidylinositol 3-kinaserelated protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. Genes & Dev. 15: 2215-2228.
250. Yamashita, A., Kashima, I., and Ohno, S. 2005. The role of SMG-1 in nonsense-mediated mRNA decay. Biochim. Biophys. Acta 1754: 305-315.
251. Zhang, X.H. and Chasin, L.A. 2004. Latent splice sites and stop codons revisited. RNA 10: 5-6.
252. Zhang, Z. and Krainer, A.R. 2004. Involvement of SR proteins in mRNA surveillance. Mol. Cell 16: 597-607.
253. Zhang, J. and Maquat, L.E. 1996. Evidence that the decay of nucleus-associated nonsense mRNA for human triosephosphate isomerase involves nonsense codon recognition after splicing. RNA 2: 235-243.
254. Zhang, J. and Maquat, L.E. 1997. Evidence that translation reinitiation abrogates nonsense-mediated mRNA decay in mammalian cells. EMBO J. 16: 826-833.
255. Zhang, S., Welch, E.M., Hogan, K., Brown, A.H., Peltz, S.W., and Jacobson, A. 1997. Polysome-associated mRNAs are substrates for the nonsense-mediated mRNA decay pathway in Saccharomyces cerevisiae. RNA 3: 234-244.
256. Zhang, J., Sun, X., Qian, Y., LaDuca, J.P., and Maquat, L.E. 1998a. At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: A possible link between nuclear splicing and cytoplasmic translation. Mol. Cell. Biol. 18: 5272-5283.
257. Zhang, J., Sun, X., Qian, Y., and Maquat, L.E. 1998b. Intron function in the nonsense-mediated decay of β-globin mRNA: Indications that pre-mRNA splicing in the nucleus can influence mRNA translation in the cytoplasm. RNA 4: 801-815.
258. Zhang, X., Lee, J., and Chasin, L.A. 2003. The effect of nonsense codons on splicing: A genomic analysis. RNA 9: 637-639.
259. Zhou, Z., Luo, M.J., Straesser, K., Katahira, J., Hurt, E., and Reed, R. 2000. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans. Nature 407: 401-405.