A conserved alternative splicing event in plants reveals an ancient exonization of 5S rRNA that regulates TFIIIA

References

• Barbazuk WB, Fu Y, McGinnis KM. Genome-wide analyses of alternative splicing in plants: Opportunities and challenges. Genome Res 2008; 18:14 - 18
   Web of Science ®Google Scholar
• Leipzig J, Pevzner P, Heber S. The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res 2004; 32:3977 - 3983
   PubMed Web of Science ®Google Scholar
• Modrek B, Lee C. A genomic view of alternative splicing. Nat Genet 2002; 30:13 - 19
   PubMed Web of Science ®Google Scholar
• Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 2009; 20:45 - 58
   PubMed Web of Science ®Google Scholar
• Gupta S, Zink D, Korn B, Vingron M, Haas SA. Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics 2004; 20:2579 - 2585
   PubMed Web of Science ®Google Scholar
• Stamm S, Ben-Ari S, Rafalska I, Tang Y, Zhang Z, Toiber D, et al. Function of alternative splicing. Gene 2005; 344:1 - 20
   PubMed Web of Science ®Google Scholar
• Belgrader P, Cheng J, Zhou X, Stephenson LS, Maquat LE. Mammalian nonsense codons can be cis effectors of nuclear mRNA half-life. Mol Cell Biol 1994; 14:8219 - 8228
   PubMed Web of Science ®Google Scholar
• Maquat LE. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nat Rev Mol Cell Biol 2004; 5:89 - 99
   PubMed Web of Science ®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
   PubMed Web of Science ®Google Scholar
• Wang BB, Brendel V. Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA 2006; 103:7175 - 7180
   PubMed Web of Science ®Google Scholar
• Melamud E, Moult J. Stochastic noise in splicing machinery. Nucleic Acids Res 2009; 37:4873 - 4886
   PubMed Web of Science ®Google Scholar
• Melamud E, Moult J. Structural implication of splicing stochastics. Nucleic Acids Res 2009; 37:4862 - 4872
   PubMed Web of Science ®Google Scholar
• Zhang Z, Xin D, Wang P, Zhou L, Hu L, Kong X, et al. Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay. BMC Biol 2009; 7:23
   PubMed Web of Science ®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
   PubMed Web of Science ®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
   PubMedGoogle Scholar
• Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, et al. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev 2007; 21:708 - 718
   PubMed Web of Science ®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
   PubMed Web of Science ®Google Scholar
• Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 2007; 446:926 - 929
   PubMed Web of Science ®Google Scholar
• Fu Y, Bannach O, Chen H, Teune JH, Schmitz A, Steger G, et al. Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA. Genome Res 2009; 19:913 - 921
   PubMed Web of Science ®Google Scholar
• Hammond MC, Wachter A, Breaker RR. A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs. Nat Struct Mol Biol 2009; 16:541 - 549
   PubMed Web of Science ®Google Scholar
• Chaw SM, Chang CC, Chen HL, Li WH. Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol 2004; 58:424 - 441
   PubMed Web of Science ®Google Scholar
• Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J. 5 S rRNA: structure and interactions. Biochem J 2003; 371:641 - 651
   PubMed Web of Science ®Google Scholar
• Engelke DR, Ng SY, Shastry BS, Roeder RG. Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes. Cell 1980; 19:717 - 728
   PubMed Web of Science ®Google Scholar
• Pelham HR, Brown DD. A specific transcription factor that can bind either the 5S RNA gene or 5S RNA. Proc Natl Acad Sci USA 1980; 77:4170 - 4174
   PubMed Web of Science ®Google Scholar
• Cassiday LA, Lebruska LL, Benson LM, Naylor S, Owen WG, Maher LJ 3rd. Binding stoichiometry of an RNA aptamer and its transcription factor target. Anal Biochem 2002; 306:290 - 297
   PubMed Web of Science ®Google Scholar
• Yoine M, Ohto MA, Onai K, Mita S, Nakamura K. The lba1 mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay causes pleiotropic phenotypic changes and altered sugar signalling in Arabidopsis. Plant J 2006; 47:49 - 62
   PubMed Web of Science ®Google Scholar
• Schwartz S, Gal-Mark N, Kfir N, Oren R, Kim E, Ast G. Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol 2009; 5:1000300
   PubMed Web of Science ®Google Scholar
• Shepard PJ, Hertel KJ. Conserved RNA secondary structures promote alternative splicing. RNA 2008; 14:1463 - 1469
   PubMed Web of Science ®Google Scholar
• Sorek R, Ast G, Graur D. Alu-containing exons are alternatively spliced. Genome Res 2002; 12:1060 - 1067
   PubMed Web of Science ®Google Scholar
• Lev-Maor G, Ram O, Kim E, Sela N, Goren A, Levanon EY, et al. Intronic Alus influence alternative splicing. PLoS Genet 2008; 4:1000204
   Web of Science ®Google Scholar
• Kalendar R, Tanskanen J, Chang W, Antonius K, Sela H, Peleg O, et al. Cassandra retrotransposons carry independently transcribed 5S RNA. Proc Natl Acad Sci USA 2008; 105:5833 - 5838
   PubMed Web of Science ®Google Scholar
• Lejeune F, Maquat LE. Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr Opin Cell Biol 2005; 17:309 - 315
   PubMed Web of Science ®Google Scholar
• McGuire AM, Pearson MD, Neafsey DE, Galagan JE. Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol 2008; 9:50
   PubMed Web of Science ®Google Scholar