Translational control of intron splicing in eukaryotes

Article metrics


Most eukaryotic genes are interrupted by non-coding introns that must be accurately removed from pre-messenger RNAs to produce translatable mRNAs1. Splicing is guided locally by short conserved sequences, but genes typically contain many potential splice sites, and the mechanisms specifying the correct sites remain poorly understood. In most organisms, short introns recognized by the intron definition mechanism2 cannot be efficiently predicted solely on the basis of sequence motifs3. In multicellular eukaryotes, long introns are recognized through exon definition2 and most genes produce multiple mRNA variants through alternative splicing4. The nonsense-mediated mRNA decay5,6 (NMD) pathway may further shape the observed sets of variants by selectively degrading those containing premature termination codons, which are frequently produced in mammals7,8. Here we show that the tiny introns of the ciliate Paramecium tetraurelia are under strong selective pressure to cause premature termination of mRNA translation in the event of intron retention, and that the same bias is observed among the short introns of plants, fungi and animals. By knocking down the two P. tetraurelia genes encoding UPF1, a protein that is crucial in NMD, we show that the intrinsic efficiency of splicing varies widely among introns and that NMD activity can significantly reduce the fraction of unspliced mRNAs. The results suggest that, independently of alternative splicing, species with large intron numbers universally rely on NMD to compensate for suboptimal splicing efficiency and accuracy.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Characteristics of P. tetraurelia introns.
Figure 2: Size distributions of the 13,050 stopless and 2,236 stop-containing introns from the EST-confirmed set.
Figure 3: Size distributions of introns in other eukaryotes.
Figure 4: Accumulation of unspliced mRNAs after UPF1 knockdown.


  1. 1

    Roy, S. W. & Gilbert, W. The evolution of spliceosomal introns: patterns, puzzles and progress. Nature Rev. Genet. 7, 211–221 (2006)

  2. 2

    Berget, S. M. Exon recognition in vertebrate splicing. J. Biol. Chem. 270, 2411–2414 (1995)

  3. 3

    Lim, L. P. & Burge, C. B. A computational analysis of sequence features involved in recognition of short introns. Proc. Natl Acad. Sci. USA 98, 11193–11198 (2001)

  4. 4

    Ast, G. How did alternative splicing evolve? Nature Rev. Genet. 5, 773–782 (2004)

  5. 5

    Conti, E. & Izaurralde, E. Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr. Opin. Cell Biol. 17, 316–325 (2005)

  6. 6

    Maquat, L. E. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nature Rev. Mol. Cell Biol. 5, 89–99 (2004)

  7. 7

    Lewis, B. P., Green, R. E. & Brenner, S. E. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl Acad. Sci. USA 100, 189–192 (2003)

  8. 8

    Pan, Q. et al. Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev. 20, 153–158 (2006)

  9. 9

    Russell, C. B., Fraga, D. & Hinrichsen, R. D. Extremely short 20–33 nucleotide introns are the standard length in Paramecium tetraurelia . Nucleic Acids Res. 22, 1221–1225 (1994)

  10. 10

    Aury, J. M. et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia . Nature 444, 171–178 (2006)

  11. 11

    Romfo, C. M., Alvarez, C. J., van Heeckeren, W. J., Webb, C. J. & Wise, J. A. Evidence for splice site pairing via intron definition in Schizosaccharomyces pombe . Mol. Cell. Biol. 20, 7955–7970 (2000)

  12. 12

    Ishigaki, Y., Li, X., Serin, G. & Maquat, L. E. Evidence for a pioneer round of mRNA translation: mRNAs subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20. Cell 106, 607–617 (2001)

  13. 13

    Galvani, A. & Sperling, L. RNA interference by feeding in Paramecium . Trends Genet. 18, 11–12 (2002)

  14. 14

    Lynch, M. The origins of eukaryotic gene structure. Mol. Biol. Evol. 23, 450–468 (2006)

  15. 15

    Mohn, F., Buhler, M. & Muhlemann, O. Nonsense-associated alternative splicing of T-cell receptor beta genes: no evidence for frame dependence. RNA 11, 147–156 (2005)

  16. 16

    Wang, J., Chang, Y. F., Hamilton, J. I. & Wilkinson, M. F. Nonsense-associated altered splicing: a frame-dependent response distinct from nonsense-mediated decay. Mol. Cell 10, 951–957 (2002)

  17. 17

    Wang, J., Hamilton, J. I., Carter, M. S., Li, S. & Wilkinson, M. F. Alternatively spliced TCR mRNA induced by disruption of reading frame. Science 297, 108–110 (2002)

  18. 18

    Miriami, E., Sperling, R., Sperling, J. & Motro, U. Regulation of splicing: the importance of being translatable. RNA 10, 1–4 (2004)

  19. 19

    Wachtel, C., Li, B., Sperling, J. & Sperling, R. Stop codon-mediated suppression of splicing is a novel nuclear scanning mechanism not affected by elements of protein synthesis and NMD. RNA 10, 1740–1750 (2004)

  20. 20

    Maquat, L. E. NASty effects on fibrillin pre-mRNA splicing: another case of ESE does it, but proposals for translation-dependent splice site choice live on. Genes Dev. 16, 1743–1753 (2002)

  21. 21

    Wilkinson, M. F. & Shyu, A. B. RNA surveillance by nuclear scanning? Nature Cell Biol. 4, E144–E147 (2002)

  22. 22

    Buhler, M., Wilkinson, M. F. & Muhlemann, O. Intranuclear degradation of nonsense codon-containing mRNA. EMBO Rep. 3, 646–651 (2002)

  23. 23

    Iborra, F. J., Escargueil, A. E., Kwek, K. Y., Akoulitchev, A. & Cook, P. R. Molecular cross-talk between the transcription, translation, and nonsense-mediated decay machineries. J. Cell Sci. 117, 899–906 (2004)

  24. 24

    Brogna, S., Sato, T. A. & Rosbash, M. Ribosome components are associated with sites of transcription. Mol. Cell 10, 93–104 (2002)

  25. 25

    Dahlberg, J. E. & Lund, E. Does protein synthesis occur in the nucleus? Curr. Opin. Cell Biol. 16, 335–338 (2004)

  26. 26

    Iborra, F. J., Jackson, D. A. & Cook, P. R. The case for nuclear translation. J. Cell Sci. 117, 5713–5720 (2004)

  27. 27

    Nathanson, L., Xia, T. & Deutscher, M. P. Nuclear protein synthesis: a re-evaluation. RNA 9, 9–13 (2003)

  28. 28

    Garnier, O., Serrano, V., Duharcourt, S. & Meyer, E. RNA-mediated programming of developmental genome rearrangements in Paramecium tetraurelia . Mol. Cell. Biol. 24, 7370–7379 (2004)

  29. 29

    Domeier, M. E. et al. A link between RNA interference and nonsense-mediated decay in Caenorhabditis elegans . Science 289, 1928–1931 (2000)

  30. 30

    Arciga-Reyes, L., Wootton, L., Kieffer, M. & Davies, B. UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis . Plant J. 47, 480–489 (2006)

  31. 31

    Hsu, F. et al. The UCSC Known Genes. Bioinformatics 22, 1036–1046 (2006)

  32. 32

    Karolchik, D. et al. The UCSC Genome Browser Database. Nucleic Acids Res. 31, 51–54 (2003)

  33. 33

    Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002)

  34. 34

    Pruitt, K. D., Tatusova, T. & Maglott, D. R. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33, D501–D504 (2005)

  35. 35

    Ashurst, J. L. et al. The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res. 33, D459–D465 (2005)

  36. 36

    Kent, W. J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002)

  37. 37

    Mott, R. EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci. 13, 477–478 (1997)

  38. 38

    Skouri, F. & Cohen, J. Genetic approach to regulated exocytosis using functional complementation in Paramecium: identification of the ND7 gene required for membrane fusion. Mol. Biol. Cell 8, 1063–1071 (1997)

  39. 39

    Gogendeau, D. et al. Functional diversification of centrins and cell morphological complexity. J. Cell Sci. 121, 65–74 (2007)

Download references


We thank V. Wood, P. Mooney and A. Tivey for providing gff files for S. pombe data, and D. Gogendeau and J. Beisson for the gift of the ICL7a feeding plasmid. This work was funded by the CNRS and by the Agence Nationale de la Recherche. K.B. was supported by a postdoctoral contract from the CNRS. Experimental work was supported by grants from the Ministère de la Recherche and the Association pour la Recherche sur le Cancer.

Author information

Correspondence to Eric Meyer.

Supplementary information

Supplementary Information

The file contains Supplementary Figures S1-S6 with Legends and Supplementary Tables 1-5. This file provides details of the statistical analyses of introns from all species examined, size distributions of introns from C. elegans, D. melanogaster and S. pombe, an evolutionary analysis of stop codon conservation in P. tetraurelia introns, and details of the UPF1 and UPF2 knockdown experiments in P. tetraurelia. (PDF 3195 kb)

Rights and permissions

Reprints and Permissions

About this article

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.