Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast

• DOI: 10.1371/journal.pgen.1005732
• Publication Date: 2015-12-14T17:58:59Z
• Authors: Jeffrey A. Hussmann; Stephanie Patchett; Arlen Johnson; Sara Sawyer; William H. Press
• Keywords: Ribosome profiling; Eukaryotic Ribosome

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