Nonsense-mediated mRNA decay: target genes and functional diversification of effectors

Trends in Biochemical Sciences

Volumn 31, Issue 11, 2006, Pages 639-646

  Rehwinkel, Jan ^a   Raes, Jeroen ^a   Izaurralde, Elisa ^a,b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA BINDING PROTEIN;

CARCINOGENESIS; COMPARATIVE GENE MAPPING; DNA REPAIR; DROSOPHILA; DRUG TARGETING; FUNCTIONAL GENOMICS; GENE CONTROL; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE MUTATION; GENETIC DISORDER; GENETIC VARIABILITY; HUMAN; HUMAN VERSUS NONHUMAN DATA; MAMMAL; NONHUMAN; NONSENSE MUTATION; ORTHOLOGY; PHENOTYPIC VARIATION; PRIORITY JOURNAL; QUALITY CONTROL; REVIEW; RNA DEGRADATION; RNA TRANSCRIPTION; TELOMERE; TRANSCRIPTION REGULATION; YEAST;

ANIMALS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; HYDROLYSIS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; TELOMERE;

EID: 33750356583     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2006.09.005     Document Type: Review

References (70)

1. Fasken M.B., and Corbett A.H. Process or perish: quality control in mRNA biogenesis. Nat. Struct. Mol. Biol. 12 (2005) 482-488
2. Conti E., and Izaurralde E. Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr. Opin. Cell Biol. 17 (2005) 316-325
3. Lejeune F., and Maquat L.E. Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr. Opin. Cell Biol. 17 (2005) 309-315
4. Baker K.E., and Parker R. Nonsense-mediated mRNA decay: terminating erroneous gene expression. Curr. Opin. Cell Biol. 16 (2004) 293-299
5. Lelivelt M.J., and Culbertson M.R. Yeast Upf proteins required for RNA surveillance affect global expression of the yeast transcriptome. Mol. Cell. Biol. 19 (1999) 6710-6719
6. He F., et al. Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast. Mol. Cell 12 (2003) 1439-1452
7. Mendell J.T., et al. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36 (2004) 1073-1078
8. Rehwinkel J., et al. Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA 11 (2005) 1530-1544
9. Wittmann J., et al. hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay. Mol. Cell. Biol. 26 (2006) 1272-1287
10. Leeds P., et al. The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes Dev. 5 (1991) 2303-2314
11. Hodgkin J., et al. A new kind of informational suppression in the nematode Caenorhabditis elegans. Genetics 123 (1989) 301-313
12. Pulak R., and Anderson P. mRNA surveillance by the Caenorhabditis elegans smg genes. Genes Dev. 7 (1993) 1885-1897
13. Page M.F., et al. SMG-2 is a phosphorylated protein required for mRNA surveillance in Caenorhabditis elegans and related to Upf1p of yeast. Mol. Cell. Biol. 19 (1999) 5943-5951
14. Gatfield D., et al. Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. EMBO J. 22 (2003) 3960-3970
15. Pal M., et al. 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 (2001) 5-15
16. Denning G., et al. Cloning of a novel phosphatidylinositol kinase-related kinase, characterization of the human SMG-1 RNA surveillance protein. J. Biol. Chem. 276 (2001) 22709-22714
17. Yamashita A., et al. Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. Genes Dev. 15 (2001) 2215-2228
18. Cali B.M., et al. smg-7 is required for mRNA surveillance in Caenorhabditis elegans. Genetics 151 (1999) 605-616
19. Anders K.R., et al. SMG-5, required for C. elegans nonsense-mediated mRNA decay, associates with SMG-2 and protein phosphatase 2A. EMBO J. 22 (2003) 641-650
20. Chiu S.Y., et al. Characterization of human Smg5/7a, a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1. RNA 9 (2003) 77-87
21. Ohnishi T., et al. Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. Mol. Cell 12 (2003) 1187-1200
22. Grimson A., et al. SMG-1 is a phosphatidylinositol kinase-related protein kinase required for nonsense-mediated mRNA decay in Caenorhabditis elegans. Mol. Cell. Biol. 24 (2004) 7483-7490
23. Fukuhara N., et al. SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway. Mol. Cell 17 (2005) 537-547
24. Kashima I., et al. 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 (2006) 355-367
25. Behm-Ansmant I., and Izaurralde E. Quality control of gene expression, a stepwise assembly pathway for the surveillance complex that triggers nonsense-mediated mRNA decay. Genes Dev. 20 (2006) 391-398
26. Nagy E., and Maquat L.E. A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. Trends Biochem. Sci. 23 (1998) 198-199
27. Le Hir H., et al. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 19 (2000) 6860-6869
28. Le Hir H., et al. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 20 (2001) 4987-4997
29. Lykke-Andersen J., et al. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. Cell 103 (2000) 1121-1131
30. Kim V.N., et al. Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex. Science 293 (2001) 1832-1836
31. Ishigaki Y., et al. 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 (2001) 607-617
32. Fribourg S., et al. A novel mode of RBD-protein recognition in the Y14-Mago complex. Nat. Struct. Biol. 10 (2003) 433-439
33. Gehring N.H., et al. Y14 and hUpf3b form an NMD-activating complex. Mol. Cell 11 (2003) 939-949
34. Gehring N.H., et al. Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. Mol. Cell 20 (2005) 65-75
35. Lykke-Andersen J., et al. Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1. Science 293 (2001) 1836-1839
36. Palacios I.M., et al. An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay. Nature 427 (2004) 753-757
37. Ferraiuolo M.A., et al. A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 4118-4123
38. Shibuya T., et al. eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat. Struct. Mol. Biol. 11 (2004) 346-351
39. Hilleren P., and Parker R. mRNA surveillance in eukaryotes: kinetic proofreading of proper translation termination as assessed by mRNP domain organization?. RNA 5 (1999) 711-719
40. Ruiz-Echevarria M.J., et al. Identifying the right stop: determining how the surveillance complex recognizes and degrades an aberrant mRNA. EMBO J. 17 (1998) 575-589
41. Amrani N., et al. A faux 3′-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay. Nature 432 (2004) 112-118
42. Muhlrad D., and Parker R. Aberrant mRNAs with extended 3′ UTRs are substrates for rapid degradation by mRNA surveillance. RNA 5 (1999) 1299-1307
43. Kebaara B., et al. The Upf-dependent decay of wild-type PPR1 mRNA depends on its 5′-UTR and first 92 ORF nucleotides. Nucleic Acids Res. 31 (2003) 3157-3165
44. Welch E.M., and Jacobson A. An internal open reading frame triggers nonsense-mediated decay of the yeast SPT10 mRNA. EMBO J. 18 (1999) 6134-6145
45. Li S., and Wilkinson M.F. Nonsense surveillance in lymphocytes?. Immunity 8 (1998) 135-141
46. Rehwinkel J., et al. Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster. Mol. Cell. Biol. 26 (2006) 2965-2975
47. Hodgetts R. Eukaryotic gene regulation by targeted chromatin re-modeling at dispersed, middle-repetitive sequence elements. Curr. Opin. Genet. Dev. 14 (2004) 680-685
48. Tatusov R.L., et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4 (2003) 41
49. Pandita T.K. ATM function and telomere stability. Oncogene 21 (2002) 611-618
50. Dahlseid J.N., et al. mRNAs encoding telomerase components and regulators are controlled by UPF genes in Saccharomyces cerevisiae. Eukaryot. Cell 2 (2003) 134-142
51. Lew J.E., et al. Telomere length regulation and telomeric chromatin require the nonsense-mediated mRNA decay pathway. Mol. Cell. Biol. 18 (1998) 6121-6130
52. Snow B.E., et al. Functional conservation of the telomerase protein Est1p in humans. Curr. Biol. 13 (2003) 698-704
53. Reichenbach P., et al. A human homolog of yeast est1 associates with telomerase and uncaps chromosome ends when overexpressed. Curr. Biol. 13 (2003) 568-574
54. Azzalin C.M., and Lingner J. The human RNA surveillance factor UPF1 is required for S phase progression and genome stability. Curr. Biol. 16 (2006) 433-439
55. Brumbaugh K.M., et al. The mRNA surveillance protein hSMG-1 functions in genotoxic stress response pathways in mammalian cells. Mol. Cell 14 (2004) 585-598
56. Kim Y.K., et al. Mammalian Staufen1 recruits Upf1 to specific mRNA 3′ UTRs so as to elicit mRNA decay. Cell 120 (2005) 195-208
57. Kaygun H., and Marzluf W.F. Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1. Nat. Struct. Mol. Biol. 12 (2005) 794-800
58. Medghalchi S.M., et al. Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. Hum. Mol. Genet. 10 (2001) 99-105
59. Holbrook J.A., et al. Nonsense-mediated decay approaches the clinic. Nat. Genet. 36 (2004) 801-808
60. Frischmeyer P.A., and Dietz H.C. Nonsense-mediated mRNA decay in health and disease. Hum. Mol. Genet. 8 (1999) 1893-1900
61. Noensie E.N., and Dietz H.C. A strategy for disease gene identification through nonsense-mediated mRNA decay inhibition. Nat. Biotechnol. 19 (2001) 434-439
62. Wolf M., et al. NMD microarray analysis for rapid genome-wide screen of mutated genes in cancer. Cell Oncol. 27 (2005) 169-173
63. Delia D., et al. MRE11 mutations and impaired ATM-dependent responses in an Italian family with ataxia-telangiectasia-like disorder. Hum. Mol. Genet. 13 (2004) 2155-2163
64. Wilschanski M., et al. Gentamicin-induced correction of CFTR function in patients with cystic fibrosis and CFTR stop mutations. N. Engl. J. Med. 349 (2003) 1433-1441
65. Rajavel K.S., and Neufeld E.F. Nonsense-mediated decay of human HEXA mRNA. Mol. Cell. Biol. 21 (2001) 5512-5519
66. Zhang J., et al. 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 (1998) 801-815
67. Buhler M., et al. EJC-independent degradation of nonsense immunoglobulin-μ mRNA depends on 3′ UTR length. Nat. Struct. Mol. Biol. 13 (2006) 462-464
68. Ruiz-Echevarria M.J., and Peltz S.W. Utilizing the GCN4 leader region to investigate the role of the sequence determinants in nonsense-mediated mRNA decay. EMBO J. 15 (1996) 2810-2819
69. Plant E.P., et al. A programmed -1 ribosomal frameshift signal can function as a cis-acting mRNA destabilizing element. Nucleic Acids Res. 32 (2004) 784-790
70. Sun X., et al. 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 (2001) 1009-1017