Chang YF, Imam JS, Wilkinson ME: The nonsense-mediated decay RNA surveillance pathway. Ann Rev Biochem. 2007, 76: 51-74. 10.1146/annurev.biochem.76.050106.093909.
Article
CAS
PubMed
Google Scholar
Conti E, Izaurralde E: Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr Opin Cell Biol. 2005, 17: 316-325. 10.1016/j.ceb.2005.04.005.
Article
CAS
PubMed
Google Scholar
Maquat LE: Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nat Rev Mol Cell Biol. 2004, 5: 89-99. 10.1038/nrm1310.
Article
CAS
PubMed
Google Scholar
Rehwinkel J, Raes J, Izaurralde E: Nonsense-mediated mRNA decay: Target genes and functional diversification of effectors. Trends Biochem Sci. 2006, 31: 639-646. 10.1016/j.tibs.2006.09.005.
Article
CAS
PubMed
Google Scholar
Kerenyi Z, Merai Z, Hiripi L, Benkovics A, Gyula P, Lacomme C, Barta E, Nagy F, Silhavy D: Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay. Embo J. 2008, 27: 1585-1595. 10.1038/emboj.2008.88.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wen J, Brogna S: Nonsense-mediated mRNA decay. Biochem Soc Trans. 2008, 36: 514-516. 10.1042/BST0360514.
Article
CAS
PubMed
Google Scholar
Shyu AB, Wilkinson MF, van Hoof A: Messenger RNA regulation: to translate or to degrade. Embo J. 2008, 27: 471-481. 10.1038/sj.emboj.7601977.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lelivelt MJ, Culbertson MR: Yeast Upf proteins required for RNA surveillance affect global expression of the yeast transcriptome. Mol Cell Biol. 1999, 19: 6710-6719.
Article
PubMed Central
CAS
PubMed
Google Scholar
He F, Li X, Spatrick P, Casillo R, Dong S, Jacobson A: Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. Mol Cell. 2003, 12: 1439-1452. 10.1016/S1097-2765(03)00446-5.
Article
CAS
PubMed
Google Scholar
Mendell JT, Sharifi NA, Meyers JL, Martinez-Murillo F, Dietz HC: Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet. 2004, 36: 1073-1078. 10.1038/ng1429.
Article
CAS
PubMed
Google Scholar
Rehwinkel J, Letunic I, Raes J, Bork P, Izaurralde E: Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA. 2005, 11: 1530-1544. 10.1261/rna.2160905.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wittmann J, Hol EM, Jack HM: hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay. Mol Cell Biol. 2006, 26: 1272-1287. 10.1128/MCB.26.4.1272-1287.2006.
Article
PubMed Central
CAS
PubMed
Google Scholar
Muhlrad D, Parker R: Aberrant mRNAs with extended 3' UTRs are substrates for rapid degradation by mRNA surveillance. RNA. 1999, 5: 1299-1307. 10.1017/S1355838299990829.
Article
PubMed Central
CAS
PubMed
Google Scholar
Amrani N, Ganesan R, Kervestin S, Mangus DA, Ghosh S, Jacobson A: A faux 3'-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay. Nature. 2004, 432: 112-118. 10.1038/nature03060.
Article
CAS
PubMed
Google Scholar
Behm-Ansmant I, Gatfield D, Rehwinkel J, Hilgers V, Izaurralde E: A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay. Embo J. 2007, 26: 1591-1601. 10.1038/sj.emboj.7601588.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nagy E, Maquat LE: A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. Trends Biochem Sci. 1998, 23: 198-199. 10.1016/S0968-0004(98)01208-0.
Article
CAS
PubMed
Google Scholar
Kuzmiak HA, Maquat LE: Applying nonsense-mediated mRNA decay research to the clinic: progress and challenges. Trends Mol Med. 2006, 12: 306-316. 10.1016/j.molmed.2006.05.005.
Article
CAS
PubMed
Google Scholar
Singh G, Rebbapragada I, Lykke-Andersen J: A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay. PLoS Biol. 2008, 6: e111-10.1371/journal.pbio.0060111.
Article
PubMed Central
PubMed
Google Scholar
Silva AL, Ribeiro P, Inacio A, Liebhaber SA, Romao L: Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense-mediated mRNA decay. RNA. 2008, 14: 563-576. 10.1261/rna.815108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Eberle AB, Stalder L, Mathys H, Orozco RZ, Muhlemann O: Posttranscriptional gene regulation by spatial rearrangement of the 3' untranslated region. PLoS Biol. 2008, 6: e92-10.1371/journal.pbio.0060092.
Article
PubMed Central
PubMed
Google Scholar
Muhlemann O: Recognition of nonsense mRNA: towards a unified model. Biochem Soc Trans. 2008, 36: 497-501. 10.1042/BST0360497.
Article
CAS
PubMed
Google Scholar
Medghalchi SM, Frischmeyer PA, Mendell JT, Kelly AG, Lawler AM, Dietz HC: Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. Hum Mol Genet. 2001, 10: 99-105. 10.1093/hmg/10.2.99.
Article
CAS
PubMed
Google Scholar
Frischmeyer PA, Dietz HC: Nonsense-mediated mRNA decay in health and disease. Hum Mol Genet. 1999, 8: 1893-1900. 10.1093/hmg/8.10.1893.
Article
CAS
PubMed
Google Scholar
Ivanov I, Lo KC, Hawthorn L, Cowell JK, Ionov Y: Identifying candidate colon cancer tumor suppressor genes using inhibition of nonsense-mediated mRNA decay in colon cancer cells. Oncogene. 2007, 26: 2873-2884. 10.1038/sj.onc.1210098.
Article
CAS
PubMed
Google Scholar
Noensie EN, Dietz HC: A strategy for disease gene identification through nonsense-mediated mRNA decay inhibition. Nat Biotechnol. 2001, 19: 434-439. 10.1038/88099.
Article
CAS
PubMed
Google Scholar
Khajavi M, Inoue K, Lupski JR: Nonsense-mediated mRNA decay modulates clinical outcome of genetic disease. Eur J Hum Genet. 2006, 14: 1074-1081. 10.1038/sj.ejhg.5201649.
Article
CAS
PubMed
Google Scholar
McGlincy NJ, Smith CW: Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?. Trends Biochem Sci. 2008, 33: 385-393. 10.1016/j.tibs.2008.06.001.
Article
CAS
PubMed
Google Scholar
Lareau LF, Brooks AN, Soergel DA, Meng Q, Brenner SE: The coupling of alternative splicing and nonsense-mediated mRNA decay. Adv Exp Med Biol. 2007, 623: 190-211.
Article
PubMed
Google Scholar
Jaillon O, Bouhouche K, Gout JF, Aury JM, Noel B, Saudemont B, Nowacki M, Serrano V, Porcel BM, Segurens B, Le Mouel A, Lepere G, Schachter V, Betermier M, Cohen J, Wincker P, Sperling L, Duret L, Meyer E: Translational control of intron splicing in eukaryotes. Nature. 2008, 451: 359-362. 10.1038/nature06495.
Article
CAS
PubMed
Google Scholar
Kurmangaliyev YZ, Gelfand MS: Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics. 2008, 9: 13-10.1186/1471-2164-9-13.
Article
PubMed Central
PubMed
Google Scholar
Viegas MH, Gehring NH, Breit S, Hentze MW, Kulozik AE: 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. 2007, 35: 4542-4551. 10.1093/nar/gkm461.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gardner LB: Hypoxic inhibition of nonsense-mediated RNA decay regulates gene expression and the integrated stress response. Mol Cell Biol. 2008, 28: 3729-3741. 10.1128/MCB.02284-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mitrovich QM, Anderson P: Unproductively spliced ribosomal protein mRNAs are natural targets of mRNA surveillance in C. elegans. Genes Dev. 2000, 14: 2173-2184. 10.1101/gad.819900.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cuccurese M, Russo G, Russo A, Pietropaolo C: Alternative splicing and nonsense-mediated mRNA decay regulate mammalian ribosomal gene expression. Nucleic Acids Res. 2005, 33: 5965-5977. 10.1093/nar/gki905.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sureau A, Gattoni R, Dooghe Y, Stevenin J, Soret J: SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs. Embo J. 2001, 20: 1785-1796. 10.1093/emboj/20.7.1785.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wollerton MC, Gooding C, Wagner EJ, Garcia-Blanco MA, Smith CW: Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol Cell. 2004, 13: 91-100. 10.1016/S1097-2765(03)00502-1.
Article
CAS
PubMed
Google Scholar
Saltzman AL, Kim YK, Pan Q, Fagnani MM, Maquat LE, Blencowe BJ: Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol. 2008, 28: 4320-4330. 10.1128/MCB.00361-08.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M: Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev. 2007, 21: 708-718. 10.1101/gad.1525507.
Article
PubMed Central
CAS
PubMed
Google Scholar
Guan Q, Zheng W, Tang S, Liu X, Zinkel RA, Tsui KW, Yandell BS, Culbertson MR: Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genet. 2006, 2: e203-10.1371/journal.pgen.0020203.
Article
PubMed Central
PubMed
Google Scholar
Lewis BP, Green RE, Brenner SE: Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci USA. 2003, 100: 189-192. 10.1073/pnas.0136770100.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pan Q, Saltzman AL, Kim YK, Misquitta C, Shai O, Maquat LE, Frey BJ, Blencowe BJ: Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev. 2006, 20: 153-158. 10.1101/gad.1382806.
Article
PubMed Central
CAS
PubMed
Google Scholar
Green RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, Garnett AT, Rio DC, Brenner SE: Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics. 2003, 19 (Suppl 1): i118-121. 10.1093/bioinformatics/btg1015.
Article
PubMed
Google Scholar
Baek D, Green P: Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc Natl Acad Sci USA. 2005, 102: 12813-12818. 10.1073/pnas.0506139102.
Article
PubMed Central
CAS
PubMed
Google Scholar
Xing Y, Lee CJ: Negative selection pressure against premature protein truncation is reduced by alternative splicing and diploidy. Trends Genet. 2004, 20: 472-475. 10.1016/j.tig.2004.07.009.
Article
CAS
PubMed
Google Scholar
Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence project: update and current status. Nucleic Acids Res. 2003, 31: 34-37. 10.1093/nar/gkg111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pruitt KD, Tatusova T, Maglott DR: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007, D61-65. 10.1093/nar/gkl842. 35 Database
Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005, D501-504. 33 Database
Johansson MJ, He F, Spatrick P, Li C, Jacobson A: Association of yeast Upf1p with direct substrates of the NMD pathway. Proc Natl Acad Sci USA. 2007, 104: 20872-20877. 10.1073/pnas.0709257105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Strausberg RL, Feingold EA, Klausner RD, Collins FS: The mammalian gene collection. Science. 1999, 286: 455-457. 10.1126/science.286.5439.455.
Article
CAS
PubMed
Google Scholar
Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, MGC Project Team: The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC). Genome Research. 2004, 14: 2121-2127. 10.1101/gr.2596504.
Article
PubMed
Google Scholar
dbSNP. [http://www.ncbi.nlm.nih.gov/projects/SNP/]
Remm M, Storm CE, Sonnhammer EL: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol. 2001, 314: 1041-1052. 10.1006/jmbi.2000.5197.
Article
CAS
PubMed
Google Scholar
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, et al: Ensembl 2008. Nucleic Acids Res. 2008, D707-714. 36 Database
Stamm S, Riethoven JJ, Le Texier V, Gopalakrishnan C, Kumanduri V, Tang Y, Barbosa-Morais NL, Thanaraj TA: ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res. 2006, D46-55. 10.1093/nar/gkj031. 34 Database
Thanaraj TA, Stamm S, Clark F, Riethoven JJ, Le Texier V, Muilu J: ASD: the Alternative Splicing Database. Nucleic Acids Res. 2004, D64-69. 10.1093/nar/gkh030. 32 Database
Kim N, Alekseyenko AV, Roy M, Lee C: The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Res. 2007, D93-98. 10.1093/nar/gkl884. 35 Database
Alekseyenko AV, Kim N, Lee CJ: Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. RNA. 2007, 13: 661-670. 10.1261/rna.325107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Modrek B, Lee CJ: Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat Genet. 2003, 34: 177-180. 10.1038/ng1159.
Article
CAS
PubMed
Google Scholar
Pan Q, Bakowski MA, Morris Q, Zhang W, Frey BJ, Hughes TR, Blencowe BJ: Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet. 2005, 21: 73-77. 10.1016/j.tig.2004.12.004.
Article
CAS
PubMed
Google Scholar
Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 1997, 13: 555-556.
CAS
PubMed
Google Scholar
Yang Z: Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol. 1998, 15: 568-573.
Article
CAS
PubMed
Google Scholar
Arbiza L, Dopazo J, Dopazo H: Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol. 2006, 2: e38-10.1371/journal.pcbi.0020038.
Article
PubMed Central
PubMed
Google Scholar
Yang Z, Nielsen R: Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 2002, 19: 908-917.
Article
CAS
PubMed
Google Scholar
Zhang J, Nielsen R, Yang Z: Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 2005, 22: 2472-2479. 10.1093/molbev/msi237.
Article
CAS
PubMed
Google Scholar
Thomas PD, Kejariwal A, Guo N, Mi H, Campbell MJ, Muruganujan A, Lazareva-Ulitsky B: Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res. 2006, W645-650. 10.1093/nar/gkl229. 34 Web Server
Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A: PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003, 13: 2129-2141. 10.1101/gr.772403.
Article
PubMed Central
CAS
PubMed
Google Scholar
Al-Shahrour F, Diaz-Uriarte R, Dopazo J: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics. 2004, 20: 578-580. 10.1093/bioinformatics/btg455.
Article
CAS
PubMed
Google Scholar
Sorek R, Safer HM: A novel algorithm for computational identification of contaminated EST libraries. Nucleic Acids Res. 2003, 31: 1067-1074. 10.1093/nar/gkg170.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M: The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008, 320: 1344-1349. 10.1126/science.1158441.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bahler J: Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature. 2008, 453: 1239-1243. 10.1038/nature07002.
Article
CAS
PubMed
Google Scholar
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921. 10.1038/35057062.
Article
CAS
PubMed
Google Scholar
Jenuth JP: The NCBI. Publicly available tools and resources on the Web. Methods Mol Biol. 2000, 132: 301-312.
CAS
PubMed
Google Scholar
National Center for Biotechnology Information. [http://www.ncbi.nlm.nih.gov/]
Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ: The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 2008, D773-779. 36 Database
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ: The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004, D493-496. 10.1093/nar/gkh103. 32 Database
The UCSC Genome Browser Database. [http://genome.ucsc.edu/]
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ihaka R, Gentleman R: R: A Language for Data Analysis and Graphics. J Comput Graph Stat. 1996, 5: 299-314. 10.2307/1390807.
Google Scholar
Benjamini Y, Yekutieli D: The control of the false discovery rate in multiple testing under dependency. Ann Statist. 2001, 29: 1165-1188. 10.1214/aos/1013699998.
Article
Google Scholar