Large-scale evidence for conservation of NMD candidature across mammals

PLoS ONE

Volumn 5, Issue 7, 2010, Pages

  de Lima Morais, David A ^a   Harrison, Paul M ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CYTOSINE; GUANINE; MESSENGER RNA; NUCLEIC ACID; POLYPEPTIDE;

ALTERNATIVE RNA SPLICING; APOPTOSIS; ARTICLE; CODON USAGE; COW; DNA CONTENT; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE MAPPING; GENE NUMBER; GENE TARGETING; GENETIC CODE; GENETIC CONSERVATION; GENETIC LINKAGE; HUMAN; INTRON RETENTION; MAMMAL; MASS SPECTROMETRY; MOUSE; NONHUMAN; NONSENSE MEDIATED MRNA DECAY; ORTHOLOGY; POPULATION GENETICS; PROTEOMICS; RAT; RNA ANALYSIS; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

ALTERNATIVE SPLICING; ANIMALS; CATTLE; CODON, NONSENSE; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; HUMANS; INTRONS; MAMMALS; MICE; RATS; RNA STABILITY;

MAMMALIA; RATTUS;

EID: 77955362158     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0011695     Document Type: Article

References (44)

1. Zavolan M, van Nimwegen E, Gaasterland T (2002) Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome Res 12: 1377-1385.
2. Brett D, Pospisil H, Valcarcel J, Reich J, Bork P (2002) Alternative splicing and genome complexity. Nat Genet 30: 29-30.
3. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, et al. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302: 2141-2144.
4. Tazi J, Bakkour N, Stamm S (2009) Alternative splicing and disease. Biochim Biophys Acta 1792: 14-26.
5. Lewis BP, Green RE, Brenner SE (2003) Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A 100: 189-192.
6. Chang YF, Imam JS, Wilkinson MF (2007) The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem 76: 51-74.
7. Silva AL, Romao L (2009) The mammalian nonsense-mediated mRNA decay pathway: to decay or not to decay! Which players make the decision? FEBS Lett 583: 499-505.
8. Holbrook JA, Neu-Yilik G, Hentze MW, Kulozik AE (2004) Nonsense-mediated decay approaches the clinic. Nat Genet 36: 801-808.
9. Le Hir H, Izaurralde E, Maquat LE, Moore MJ (2000) The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. Embo J 19: 6860-6869.
10. Saltzman AL, Kim YK, Pan Q, Fagnani MM, Maquat LE, et al. (2008) Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol 28: 4320-4330.
11. Kaygun H, Marzluff WF (2005) Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1. Nat Struct Mol Biol 12: 794-800.
12. Zhang Z, Xin D, Wang P, Zhou L, Hu L, et al. (2009) Noisy splicing, more than expression regulation, explains why some exons are subject to nonsensemediated mRNA decay. BMC Biol 7: 23.
13. Morais DD, Harrison PM (2009) Genomic evidence for non-random endemic populations of decaying exons from mammalian genes. BMC Genomics 10: 309.
14. Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE (2007) Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446: 926-929.
15. Galante PA, Sakabe NJ, Kirschbaum-Slager N, de Souza SJ (2004) Detection and evaluation of intron retention events in the human transcriptome. Rna 10: 757-765.
16. Kurmangaliyev YZ, Gelfand MS (2008) Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics 9: 13.
17. Hiller M, Huse K, Platzer M, Backofen R (2005) Non-EST based prediction of exon skipping and intron retention events using Pfam information. Nucleic Acids Res 33: 5611-5621.
18. Jaillon O, Bouhouche K, Gout JF, Aury JM, Noel B, et al. (2008) Translational control of intron splicing in eukaryotes. Nature 451: 359-362.
19. Berget SM (1995) Exon recognition in vertebrate splicing. J Biol Chem 270: 2411-2414.
20. Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J (2005) BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res 33: W460-464.
21. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-261.
22. Wingender E (2008) The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform 9: 326-332.
23. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M (2009) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res.
24. Neer EJ, Schmidt CJ, Nambudripad R, Smith TF (1994) The ancient regulatory-protein family of WD-repeat proteins. Nature 371: 297-300.
25. Green RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, et al. (2003) Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics 19 Suppl 1: i118-121.
26. Kuenen BC, Pinedo HM (2003) [New oncological treatment principle with imatinib]. Ned Tijdschr Geneeskd 147: 2044-2045.
27. Peng XD, Xu PZ, Chen ML, Hahn-Windgassen A, Skeen J, et al. (2003) Dwarfism, impaired skin development, skeletal muscle atrophy, delayed bone development, and impeded adipogenesis in mice lacking Akt1 and Akt2. Genes Dev 17: 1352-1365.
28. Yujiri T, Sather S, Fanger GR, Johnson GL (1998) Role of MEKK1 in cell survival and activation of JNK and ERK pathways defined by targeted gene disruption. Science 282: 1911-1914.
29. Merdzhanova G, Edmond V, De Seranno S, Van den Broeck A, Corcos L, et al. (2008) E2F1 controls alternative splicing pattern of genes involved in apoptosis through upregulation of the splicing factor SC35. Cell Death Differ 15: 1815-1823.
30. Mercatante D, Kole R (2000) Modification of alternative splicing pathways as a potential approach to chemotherapy. Pharmacol Ther 85: 237-243.
31. Hayes GM, Carrigan PE, Beck AM, Miller LJ (2006) Targeting the RNA splicing machinery as a novel treatment strategy for pancreatic carcinoma. Cancer Res 66: 3819-3827.
32. Stephenson LS, Maquat LE (1996) Cytoplasmic mRNA for human triosephosphate isomerase is immune to nonsense-mediated decay despite forming polysomes. Biochimie 78: 1043-1047.
33. Kerem E (2004) Pharmacologic therapy for stop mutations: how much CFTR activity is enough? Curr Opin Pulm Med 10: 547-552.
34. Ainsworth C (2005) Nonsense mutations: running the red light. Nature 438: 726-728.
35. Kuzmiak HA, Maquat LE (2006) Applying nonsense-mediated mRNA decay research to the clinic: progress and challenges. Trends Mol Med 12: 306-316.
36. Vizcaino JA, Cote R, Reisinger F, Barsnes H, Foster JM, et al. The Proteomics Identifications database: 2010 update. Nucleic Acids Res 38: D736-742.
37. Ovcharenko I, Nobrega MA, Loots GG, Stubbs L (2004) ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res 32: W280-286.
38. Malygin AA, Parakhnevitch NM, Ivanov AV, Eperon IC, Karpova GG (2007) Human ribosomal protein S13 regulates expression of its own gene at the splicing step by a feedback mechanism. Nucleic Acids Res 35: 6414-6423.
39. Shi Y, Zhai H, Wang X, Han Z, Liu C, et al. (2004) Ribosomal proteins S13 and L23 promote multidrug resistance in gastric cancer cells by suppressing druginduced apoptosis. Exp Cell Res 296: 337-346.
40. Fewell SW, Woolford JL, Jr. (1999) Ribosomal protein S14 of Saccharomyces cerevisiae regulates its expression by binding to RPS14B pre-mRNA and to 18S rRNA. Mol Cell Biol 19: 826-834.
41. Mitrovich QM, Anderson P (2000) Unproductively spliced ribosomal protein mRNAs are natural targets of mRNA surveillance in C. elegans. Genes Dev 14: 2173-2184.
42. Tatusova TA, Madden TL (1999) BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174: 247-250.
43. Wu TD, Watanabe CK (2005) GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21: 1859-1875.
44. Slater GS, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.