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Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation

Abstract

A fundamental aspect of the biogenesis and function of eukaryotic messenger RNA is the quality control systems that recognize and degrade non-functional mRNAs. Eukaryotic mRNAs where translation termination occurs too soon (nonsense-mediated decay)1 or fails to occur (non-stop decay)2 are rapidly degraded. We show that yeast mRNAs with stalls in translation elongation are recognized and targeted for endonucleolytic cleavage, referred to as ‘no-go decay’. The cleavage triggered by no-go decay is dependent on translation and involves Dom34p and Hbs1p. Dom34p and Hbs1p are similar to the translation termination factors eRF1 and eRF3 (refs 3, 4), indicating that these proteins might function in recognizing the stalled ribosome and triggering endonucleolytic cleavage. No-go decay provides a mechanism for clearing the cell of stalled translation elongation complexes, which could occur as a result of damaged mRNAs or ribosomes, or as a mechanism of post-transcriptional control.

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Figure 1: Stalling of elongating ribosomes leads to endonucleolytic cleavage of the PGK1-SL reporter transcript.
Figure 2: NGD is initiated by endonucleolytic cleavage of mRNA with various ribosomal stalls.
Figure 3: NGD is dependent on translation by ribosomes.
Figure 4: Dom34p and Hbs1p affect NGD.

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Acknowledgements

We thank P. Farabaugh for the pJD375 plasmid; A. van Hoof for strains; and members of the Parker laboratory, especially K. Baker and C. Decker, for discussions. This study was supported by funds from the Howard Hughes Medical Institute and the National Institutes of Health.

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Correspondence to Roy Parker.

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Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

This file contains the Supplementary Methods, Supplementary Discussion and the Supplementary Figure Legends. (DOC 32 kb)

Supplementary Figure 1

This figure shows that the PGK1 mRNA with ribosomal stall site is destabilized independent of the major mRNA decay pathways in yeast. (PDF 330 kb)

Supplementary Figure 2

This figure shows that 5′ and 3′ fragments accumulate specifically in ski7δ and xrn1δ strains. (PDF 130 kb)

Supplementary Figure 3

This figure shows that No-Go decay triggers endonucleolytic cleavage in the vicinity of the stall site. (PDF 535 kb)

Supplementary Figure 4

This figure shows the precursor relationship of full length and mRNA decay fragment. (PDF 459 kb)

Supplementary Figure 5

This figure shows that No-Go decay is independent of deadenylation. (PDF 317 kb)

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Doma, M., Parker, R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440, 561–564 (2006). https://doi.org/10.1038/nature04530

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