Heritability in the efficiency of nonsense-mediated mRNA decay in humans

PLoS ONE

Volumn 5, Issue 7, 2010, Pages

  Seoighe, Cathal ^a,b   Gehring, Chris ^c  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

^c KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; DCP1A PROTEIN, HUMAN; RIBONUCLEASE; TRANSACTIVATOR PROTEIN;

ARTICLE; BIOINFORMATICS; CHROMOSOME 3; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC MARKER; GENOTYPE; HAPLOTYPE MAP; HERITABILITY; HUMAN; INTRON; NONSENSE MEDIATED MRNA DECAY; PHENOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM; DNA MICROARRAY; GENETICS; RNA STABILITY; STOP CODON;

EUKARYOTA;

CODON, NONSENSE; ENDORIBONUCLEASES; EXPRESSED SEQUENCE TAGS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; INTRONS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA STABILITY; TRANS-ACTIVATORS;

EID: 77955390643     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0011657     Document Type: Article

References (45)

1. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, et al. (2003) Genome-Wide Survey of Human Pre-mRNA Splicing with Exon Junction Microarrays. Science 302: 2141-2144.
2. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
3. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
4. Nembaware V, Wolfe KH, bettoni F, Kelso J, Seoighe C (2004) Allele-specific transcript isoforms in human. FEBS Lett 577: 233-238.
5. Pagani F, Baralle FE (2004) Genomic variants in exons and introns: identifying the splicing spoilers. NatRevGenet 5: 389-396.
6. Wang GS, Cooper TA (2007) Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 8: 749-761.
7. Lopez-Bigas N, Audit B, Ouzounis C, Parra G, Guigo R (2005) Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett 579: 1900-1903.
8. Nembaware V, Lupindo B, Schouest K, Spillane C, Scheffler K, et al. (2008) Genome-wide survey of allele-specific splicing in humans. BMC Genomics 9: 265.
9. Heinzen EL, Ge D, Cronin KD, Maia JM, Shianna KV, et al. (2008) Tissuespecific genetic control of splicing: implications for the study of complex traits. PLoS Biol 6: e1.
10. Kwan T, Benovoy D, Dias C, Gurd S, Provencher C, et al. (2008) Genome-wide analysis of transcript isoform variation in humans. NatGenet 40: 225-231.
11. Kwan T, Benovoy D, Dias C, Gurd S, Serre D, et al. (2007) Heritability of alternative splicing in the human genome. Genome Res 17: 1210-1218.
12. Kwan T, Grundberg E, Koka V, Ge B, Lam KC, et al. (2009) Tissue effect on genetic control of transcript isoform variation. PLoS Genet 5: e1000608.
13. Hull J, Campino S, Rowlands K, Chan MS, Copley RR, et al. (2007) Identification of common genetic variation that modulates alternative splicing. PLoS Genet 3: e99.
14. ElSharawy A, Hundrieser B, Brosch M, Wittig M, Huse K, et al. (2009) Systematic evaluation of the effect of common SNPs on pre-mRNA splicing. Hum Mutat 30: 625-632.
15. ElSharawy A, Manaster C, Teuber M, Rosenstiel P, Kwiatkowski R, et al. (2006) SNPSplicer: systematic analysis of SNP-dependent splicing in genotyped cDNAs. Hum Mutat 27: 1129-1134.
16. Cheung VG, Spielman RS (2009) Genetics of human gene expression: mapping DNA variants that influence gene expression. Nat Rev Genet 10: 595-604.
17. Herrick D, Parker R, Jacobson A (1990) Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae. Mol Cell Biol 10: 2269-2284.
18. Wilusz CJ, Wormington M, Peltz SW (2001) The cap-to-tail guide to mRNA turnover. Nat Rev Mol Cell Biol 2: 237-246.
19. Seko Y, Cole S, Kasprzak W, Shapiro BA, Ragheb JA (2006) The role of cytokine mRNA stability in the pathogenesis of autoimmune disease. Autoimmun Rev 5: 299-305.
20. Beelman CA, Stevens A, Caponigro G, LaGrandeur TE, Hatfield L, et al. (1996) An essential component of the decapping enzyme required for normal rates of mRNA turnover. Nature 382: 642-646.
21. Hentze MW, Kulozik AE (1999) A perfect message: RNA surveillance and nonsense-mediated decay. Cell 96: 307-310.
22. Jaillon O, Bouhouche K, Gout JF, Aury JM, Noel B, et al. (2008) Translational control of intron splicing in eukaryotes. Nature 451: 359-362.
23. Zetoune AB, Fontaniere S, Magnin D, Anczukow O, Buisson M, et al. (2008) Comparison of nonsense-mediated mRNA decay efficiency in various murine tissues. BMC Genet 9: 83.
24. Bateman JF, Freddi S, Nattrass G, 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.
25. Linde L, Boelz S, Neu-Yilik G, Kulozik AE, Kerem B (2007) The efficiency of nonsense-mediated mRNA decay is an inherent character and varies among different cells. Eur J Hum Genet 15: 1156-1162.
26. Viegas MH, Gehring NH, Breit S, Hentze MW, Kulozik AE (2007) The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway. Nucleic Acids Res 35: 4542-4551.
27. Holbrook JA, Neu-Yilik G, Hentze MW, Kulozik AE (2004) Nonsense-mediated decay approaches the clinic. Nat Genet 36: 801-808.
28. Khajavi M, Inoue K, Lupski JR (2006) Nonsense-mediated mRNA decay modulates clinical outcome of genetic disease. Eur J Hum Genet 14: 1074-1081.
29. Linde L, Boelz S, Nissim-Rafinia M, Oren YS, Wilschanski M, et al. (2007) Nonsense-mediated mRNA decay affects nonsense transcript levels and governs response of cystic fibrosis patients to gentamicin. J Clin Invest 117: 683-692.
30. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
31. Franks TM, Lykke-Andersen J (2008) The control of mRNA decapping and Pbody formation. Mol Cell 32: 605-615.
32. Lykke-Andersen J (2002) Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol Cell Biol 22: 8114-8121.
33. Huang RS, Duan S, Bleibel WK, Kistner EO, Zhang W, et al. (2007) A genomewide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. ProcNatlAcadSciUSA 104: 9758-9763.
34. Friedel CC, Dölken L, Ruzsics Z, Koszinowski UH, Zimmer R (2009) Conserved principles of mammalian transcriptional regulation revealed by RNA halflife. Nucleic Acids Res 37.
35. HapMap (2003) The International HapMap Project Nature 426: 789-796.
36. Akey JM, Biswas S, Leek JT, Storey JD (2007) On the design and analysis of gene expression studies in human populations. Nat Genet 39: 807-808; author reply 808-809.
37. Chaix R, Cao C, Donnelly P (2008) Is mate choice in humans MHC-dependent? PLoS Genet 4: e1000184.
38. Dabney A, Storey JD, with assistance from Warnes GR (2009) qvalue: Q-value estimation for false discovery rate control. R package version 1.18.0.
39. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. ProcNatlAcadSciUSA 100: 9440-9445.
40. Hatfield L, Beelman CA, Stevens A, Parker R (1996) Mutations in trans-acting factors affecting mRNA decapping in Saccharomyces cerevisiae. Mol Cell Biol 16: 5830-5838.
41. Couttet P, Grange T (2004) Premature termination codons enhance mRNA decapping in human cells. Nucleic Acids Res 32: 488-494.
42. Mitrovich QM, Anderson P (2005) mRNA surveillance of expressed pseudogenes in C. elegans. Curr Biol 15: 963-967.
43. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
44. Clark TA, Schweitzer AC, Chen TX, Staples MK, Lu G, et al. (2007) Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol 8: R64.
45. Aulchenko Y, Struchalin M (2009) GenABEL: genome-wide SNP association analysis.