Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments
Autor: | Puneet Sharma, Benedikt S. Nilges, Sebastian A. Leidel, Jie Wu |
---|---|
Jazyk: | angličtina |
Rok vydání: | 2021 |
Předmět: |
Science
ved/biology.organism_classification_rank.species General Physics and Astronomy Computational biology Saccharomyces cerevisiae Cycloheximide Ribosome General Biochemistry Genetics and Molecular Biology Article chemistry.chemical_compound Mice Bias Species Specificity 540 Chemistry Animals Humans Ribosome profiling Model organism Codon Protein Synthesis Inhibitors Multidisciplinary Chemistry ved/biology RNA Translation (biology) General Chemistry Yeast HEK293 Cells Protein Biosynthesis 570 Life sciences biology Ribosomes |
Zdroj: | Sharma, Puneet; Wu, Jie; Nilges, Benedikt S.; Leidel, Sebastian A. (2021). Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments. Nature Communications, 12(1), p. 5094. Springer Nature 10.1038/s41467-021-25411-y Nature Communications Nature Communications, Vol 12, Iss 1, Pp 1-13 (2021) |
Popis: | Ribosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments. Ribosome profiling has become the gold standard to analyze mRNA translation dynamics, and the translation inhibitor cycloheximide (CHX) is often used in its application. Here the authors systematically demonstrate that CHX does not bias the outcome of ribosome profiling experiments in most organisms. |
Databáze: | OpenAIRE |
Externí odkaz: |