Translational control of intron splicing in eukaryotes

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Abstract

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.

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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.

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Acknowledgements

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.

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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)

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