Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets

RNA

Volumn 11, Issue 10, 2005, Pages 1530-1544

  Rehwinkel, Jan ^a   Letunic, Ivica ^a   Raes, Jeroen ^a   Bork, Peer ^a   Izaurralde, Elisa ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Est1; mRNA decay; mRNA surveillance; NMD; SMG; Telomeres; UPF

Indexed keywords

MESSENGER RNA;

ARTICLE; CELL PROLIFERATION; CONTROLLED STUDY; DROSOPHILA; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; METAZOON; MOLECULAR EVOLUTION; NONHUMAN; ORTHOLOGY; PHENOTYPIC VARIATION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN TARGETING; REGULATORY RNA SEQUENCE; RNA TRANSLATION; SPECIES DIFFERENCE; STOP CODON;

ANIMALS; CELL PROLIFERATION; CODON, NONSENSE; DROSOPHILA; FEEDBACK, BIOCHEMICAL; FLOW CYTOMETRY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, INSECT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA INTERFERENCE; RNA STABILITY; RNA, DOUBLE-STRANDED; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

METAZOA; NEMATODA;

EID: 25844435702     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.2160905     Document Type: Article

References (52)

1. 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.
2. Ashburner, M., Ball, C.A., Blake, J. A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al. 2000. Gene ontology: Tool for the unification of biology. Nat. Genet. 25: 25-29.
3. Baker, K.E. and Parker, R. 2004. Nonsense-mediatedmRNA decay: Terminating erroneous gene expression. Curr. Opin. Cell. Biol. 16: 293-299.
4. Boggs, R.T., Gregor, P., Idriss, S., Belote, J.M., and McKeown, M. 1987. Regulation of sexual differentiation in D. melanogaster via alternative splicing of RNA from the transformer gene. Cell 50: 739-747.
5. 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.
6. 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.
7. 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 http://www.genetics.org/cgi/rapidpdf/genetics.105. 045674v1.
8. 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.
9. Conti, E. and Izaurralde, E. 2005. Nonsense-mediated mRNA decay: Molecular insights and mechanistic variations across species. Curr. Opin. Cell. Biol. 17: 316-325.
10. Dahlseid, J.N., Lew-Smith, J., Lelivelt, M.J., Enomoto, S., Ford, A., Desruisseaux, M., McClellan, M., Lue, N., Culbertson, M.R., and Berman, J. 2003. mRNAs encoding telomerase components and regulators are controlled by UPF genes in Saccharomyces cerevisiae. Eukaryot. Cell 2: 134-142.
11. 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.
12. Domeier, M.E., Morse, D.P., Knight, S.W., Portereiko, M., Bass, B.L., and Mango, S.E. 2000. A link between RNA interference and nonsense-mediated decay in Caenorhabditis elegans. Science 289: 1928-1931.
13. 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 18: 537-547.
14. Gatfield, D. and Izaurralde, E. 2004. Nonsense-mediated mRNA decay is initiated by endonucleolytic cleavage in Drosophila. Nature 429: 575-578.
15. 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.
16. Green, R.E., Lewis, B.P., Hillman, R.T., Blanchette, M., Lareau, L.F., Garnett, A.T., Rio, D.C., and Brenner, SE. 2003.Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics 1: I118-I121.
17. 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. 17: 7483-7490.
18. Halestrap, A.P. and Price, N.T. 1999. The proton-linked monocarboxylate transporter (MCT) family: Structure, function and regulation. Biochem. J. 343: 281-299.
19. Harbison, S.T., Chang, S., Kamdar, K.P., and Mackay, T.F. 2005. Quantitative genomics of starvation stress resistance in Drosophila. Genome Biol. 6: R36.
20. 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.
21. Herold, A., Klimenko, T, and Izaurralde, E. 2001. NXF1/p15 heterodimers are essential for mRNA nuclear export in Drosophila. RNA 7: 1768-1780.
22. 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.
23. 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.
24. Ivanov, I.P., Simin, K., Letsou, A., Atkins, J.F., and Gesteland, R.F. 1998. The Drosophila gene for antizyme requires ribosomal frameshifting for expression and contains an intronic gene for snRNP Sm D3 on the opposite strand. Mol. Cell. Biol. 18: 1553-1561.
25. Kim, J.K., Gabel, H.W., Kamath, R.S., Tewari, M., Pasquinelli, A., Rual, J.F., Kennedy, S., Dybbs, M., Bertin, N., Kaplan, J.M., et al. 2005a. Functional genomic analysis of RNA interference in C. elegans. Science 308: 1164-1167.
26. Kim, Y.K., Furic, L., Desgroseillers, L., and Maquat, L.E. 2005b. Mammalian Staufen1 recruits Upf1 to specific mRNA 3′UTRs so as to elicit mRNA decay. Cell 120: 195-208.
27. 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.
28. 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.
29. 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.
30. Lew, J.E., Enomoto, S., and Berman, J. 1998. Telomere length regulation and telomeric chromatin require the nonsense-mediated mRNA decay pathway. Mol. Cell. Biol. 18: 6121-6130.
31. Lewis, B.P., Green R.E., and Brenner S.E. 2003. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl. Acad. Sci. 100: 189-192.
32. Medghalchi, S.M., Frischmeyer, P.A., Mendell, J.T., Kelly, A.G., Lawler, A.M., and Dietz, H.C. 2001. Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. Hum. Mol. Genet. 10: 99-105.
33. 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.
34. Nachman, M.W. 2002. Variation in recombination rate across the genome: Evidence and implications. Curr. Opin. Genet. Dev. 12: 657-663.
35. Ohi, R. and Gould, K.L. 1999. Regulating the onset of mitosis. Curr. Opin. Cell. Biol. 11: 267-273.
36. 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.
37. 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.
38. 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.
39. Pandita, T.K. 2002. ATM function and telomere stability. Oncogene 21: 611-618.
40. Pulak, R. and Anderson, P. 1993. mRNA surveillance by the Caenorhabditis elegans smg genes. Genes & Dev. 7: 1885-1897.
41. Rehwinkel, J., Herold, A., Gari, K., Kocher, T., Rode, M., Ciccarelli, F.L., Wilm, M., and Izaurralde, E. 2004. Genome-wide analysis of mRNAs regulated by the THO complex in Drosophila melanogaster. Nat. Struct. Mol. Biol. 11: 558-566.
42. Rehwinkel, J., Behm-Ansmant, I., Gatfield, D., and Izaurralde, E. 2005. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA (in press).
43. Reichenbach, P., Hoss, M., Azzalin, C.M., Nabholz, M., Bucher, P., and Lingner, J. 2003. A human homolog of yeast est1 associates with telomerase and uncaps chromosome ends when overexpressed. Curr. Biol. 13: 568-574.
44. Roignant, J.Y., Carre, C., Mugat, B., Szymczak, D., Lepesant, J.A., and Antoniewski, C. 2003. Absence of transitive and systemic pathways allows cell-specific and isoform-specific RNAi in Drosophila. RNA 9: 299-308.
45. Sato, M., Umeki, H., Saito, R., Kanai, A., and Tomita, M. 2003. Computational analysis of stop codon readthrough in D. melanogaster. Bioinformatics 19: 1371-1380.
46. Snow, B.E., Erdmann, N., Cruickshank, J., Goldman, H., Gill, R.M., Robinson, M.O., and Harrington, L. 2003. Functional conservation of the telomerase protein Est1p in humans. Curr. Biol. 13: 698-704.
47. Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278: 631-637.
48. von Mering, C., Jensen, L.J., Snel B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A., and Bork, P. 2005. STRING: Known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 33: D433-D437.
49. Xing. Y. and Lee, C.J. 2004. Negative selection pressure against premature protein truncation is reduced by alternative splicing and diploidy. Trends Genet. 20: 472-475.
50. Yamashita, A., Ohnishi, T., Kashima, I., Taya, Y., and Ohno, S. 2001. 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: 2215-2228.
51. Zhou, J., Hidaka, K., and Futcher, B. 2000. The Est1 subunit of yeast telomerase binds the Tlc1 telomerase RNA. Mol. Cell. Biol. 20: 1947-1955.
52. Zinke, I., Schutz, C.S., Katzenberger, J.D., Bauer, M., and Pankratz, M.J. 2002. Nutrient control of gene expression in Drosophila: Microarray analysis of starvation and sugar-dependent response. EMBO J. 21: 6162-6173.