Translation inhibitors cause abnormalities in ribosome profiling experiments

Ribosome profiling and high-throughput sequencing provide unprecedented opportunities for the analysis of mRNA translation. Using this novel method, several studies have demonstrated the widespread role of short upstream reading frames in translational control as well as slower elongation at the beg...

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Vydáno v:	Nucleic acids research Ročník 42; číslo 17; s. e134
Hlavní autoři:	Gerashchenko, Maxim V., Gladyshev, Vadim N.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	England Oxford University Press 29.09.2014
Témata:	Cycloheximide - pharmacology Heat-Shock Response - genetics High-Throughput Nucleotide Sequencing Methods Online Oxidative Stress - genetics Protein Biosynthesis - drug effects Protein Synthesis Inhibitors - pharmacology Ribosomes - drug effects Ribosomes - metabolism RNA, Messenger - chemistry RNA, Messenger - metabolism Saccharomyces cerevisiae - drug effects Saccharomyces cerevisiae - genetics Sequence Analysis, RNA
ISSN:	0305-1048, 1362-4962, 1362-4962
On-line přístup:	Získat plný text
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Popis
Shrnutí:	Ribosome profiling and high-throughput sequencing provide unprecedented opportunities for the analysis of mRNA translation. Using this novel method, several studies have demonstrated the widespread role of short upstream reading frames in translational control as well as slower elongation at the beginning of open reading frames in response to stress. Based on the initial studies, the importance of adding or omitting translation inhibitors, such as cycloheximide, was noted as it markedly affected ribosome coverage profiles. For that reason, many recent studies omitted translation inhibitors in the culture medium. Here, we investigate the influence of ranging cycloheximide concentrations on ribosome profiles in Saccharomyces cerevisiae and demonstrate that increasing the drug concentration can overcome some of the artifacts. We subjected cells to various manipulations and show that neither oxidative stress nor heat shock nor amino acid starvation affect translation elongation. Instead, the observations in the initial studies are the result of cycloheximide-inflicted artifacts. Likewise, we find little support for short upstream reading frames to be involved in widespread protein synthesis regulation under stress conditions. Our study highlights the need for better standardization of ribosome profiling methods.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0305-1048 1362-4962 1362-4962
DOI:	10.1093/nar/gku671