Sep 30, 2015

Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast

BioRxiv : the Preprint Server for Biology
Jeffrey A HussmannWilliam H Press

Abstract

Ribosome profiling produces snapshots of the locations of actively translating ribosomes on messenger RNAs. These snapshots can be used to make inferences about translation dynamics. Recent ribosome profiling studies in yeast, however, have reached contradictory conclusions regarding the average translation rate of each codon. Some experiments have used cycloheximide (CHX) to stabilize ribosomes before measuring their positions, and these studies all counterintuitively report a weak negative correlation between the translation rate of a codon and the abundance of its cognate tRNA. In contrast, some experiments performed without CHX report strong positive correlations. To explain this contradiction, we identify unexpected patterns in ribosome density downstream of each type of codon in experiments that use CHX. These patterns are evidence that elongation continues to occur in the presence of CHX but with dramatically altered codon-specific elongation rates. The measured positions of ribosomes in these experiments therefore do not reflect the amounts of time ribosomes spend at each position in vivo. These results suggest that conclusions from experiments in yeast using CHX may need reexamination. In particular, we show that in al...Continue Reading

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Mentioned in this Paper

Study
In Vivo
Patterns
MT-TA gene
Triplet Codon-amino Acid Adaptor Activity
Yeasts
Molecular Profiling
Transfer RNA
Protein Biosynthesis
Chlorhexidine

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