A novel function for alternative polyadenylation as a rescue pathway from NMD surveillance

Biochemical and Biophysical Research Communications

Volumn 353, Issue 2, 2007, Pages 487-492

  Gilat, Roi ^a   Shweiki, Dorit ^a  

^a ACADEMIC COLLEGE OF TEL AVIV YAFFO   (Israel)

Author keywords

Alternative polyadenylation; NMD rescue mechanism; Nonsense mediated mRNA decay; PTC containing transcripts

Indexed keywords

MESSENGER RNA;

ARTICLE; CONTROLLED STUDY; EXON; EXPRESSED SEQUENCE TAG; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN GENOME; HUMAN TISSUE; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; PSEUDOGENE; RNA DEGRADATION; SCREENING; STATISTICAL ANALYSIS; STOP CODON;

CHROMOSOME MAPPING; CODON, NONSENSE; GENOME, HUMAN; HUMANS; POLYADENYLATION; RNA STABILITY; TRANSCRIPTION FACTORS;

EID: 33845785665     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.12.052     Document Type: Article

References (31)

1. Mendell J.T., Sharifi N.A., Meyers J.L., Martinez-Murillo F., and Dietz H.C. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36 (2004) 1073-1078
2. Maquat L.E. Nonsense-mediated mRNA decay in mammals. J. Cell Sci. 118 (2005) 1773-1776
3. 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
4. Lejeune F., Ranganathan A.C., and Maquat L.E. eIF4G is required for the pioneer round of translation in mammalian cells. Nat. Struct. Mol. Biol. 11 (2004) 992-1000
5. Le Hir H., Izaurralde E., Maquat L.E., and Moore M.J. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 19 (2000) 6860-6869
6. Conti E., and Izaurralde E. Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr. Opin. Cell Biol. 17 (2005) 316-325
7. Khajavi M., Inoue K., and Lupski J.R. Nonsense-mediated mRNA decay modulates clinical outcome of genetic disease. Eur. J. Hum. Genet. 14 (2006) 1074-1081
8. Frischmeyer P.A., and Dietz H.C. Nonsense-mediated mRNA decay in health and disease. Hum. Mol. Genet. 8 (1999) 1893-1900
9. Lewis B.P., Green R.E., and Brenner S.E. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl. Acad. Sci. USA 100 (2003) 189-192
10. Green R.E., Lewis B.P., Hillman R.T., Blanchette M., Lareau L.F., Garnett A.T., Rio D.C., and Brenner S.E. Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics 19 Suppl. 1 (2003) i118-i121
11. Morris D.R., and Geballe A.P. Upstream open reading frames as regulators of mRNA translation. Mol. Cell Biol. 20 (2000) 8635-8642
12. Meijer H.A., and Thomas A.A. Control of eukaryotic protein synthesis by upstream open reading frames in the 5′-untranslated region of an mRNA. Biochem. J. 367 (2002) 1-11
13. Chester A., Somasekaram A., Tzimina M., Jarmuz A., Gisbourne J., O'Keefe R., Scott J., and Navaratnam N. The apolipoprotein B mRNA editing complex performs a multifunctional cycle and suppresses nonsense-mediated decay. EMBO J. 22 (2003) 3971-3982
14. Blanc V., and Davidson N.O. C-to-U RNA editing: mechanisms leading to genetic diversity. J. Biol. Chem. 278 (2003) 1395-1398
15. Stockklausner C., Breit S., Neu-Yilik G., Echner N., Hentze M.W., Kulozik A.E., and Gehring N.H. The uORF-containing thrombopoietin mRNA escapes nonsense-mediated decay (NMD). Nucleic Acids Res. 34 (2006) 2355-2363
16. Mazumder B., Seshadri V., and Fox P.L. Translational control by the 3′-UTR: the ends specify the means. Trends Biochem. Sci. 28 (2003) 91-98
17. Decker C.J., and Parker R. Diversity of cytoplasmic functions for the 3′ untranslated region of eukaryotic transcripts. Curr. Opin. Cell Biol. 7 (1995) 386-392
18. Beaudoing E., Freier S., Wyatt J.R., Claverie J.M., and Gautheret D. Patterns of variant polyadenylation signal usage in human genes. Genome Res. 10 (2000) 1001-1010
19. Tian B., Hu J., Zhang H., and Lutz C.S. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 33 (2005) 201-212
20. Zarudnaya M.I., Kolomiets I.M., Potyahaylo A.L., and Hovorun D.M. Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res. 31 (2003) 1375-1386
21. Pauws E., van Kampen A.H., van de Graaf S.A., de Vijlder J.J., and Ris-Stalpers C. Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. Nucleic Acids Res. 29 (2001) 1690-1694
22. Beaudoing E., and Gautheret D. Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res. 11 (2001) 1520-1526
23. Gilat R., Goncherov S., Esterman N., and Shweiki D. Under-representation of PolyA/PolyT tailed ESTs in human ESTdb: an obstacle to alternative polyadenylation inference. Bioinformation 1 (2006) 220-224
24. Edwalds-Gilbert G., Veraldi K.L., and Milcarek C. Alternative poly(A) site selection in complex transcription units: means to an end?. Nucleic Acids Res. 25 (1997) 2547-2561
25. Yan J., and Marr T.G. Computational analysis of 3′-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. Genome Res. 15 (2005) 369-375
26. Tabaska J.E., and Zhang M.Q. Detection of polyadenylation signals in human DNA sequences. Gene 231 (1999) 77-86
27. Gautheret D., and Lambert A. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J. Mol. Biol. 313 (2001) 1003-1011
28. Boguski M.S., Lowe T.M., and Tolstoshev C.M. dbEST-database for "expressed sequence tags". Nat. Genet. 4 (1993) 332-333
29. A.F.A. Smit, R. Hubley, P. Green, unpublished data.
30. Jurka J., Kapitonov V.V., Pavlicek A., Klonowski P., Kohany O., and Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110 (2005) 462-467
31. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410