Journal
NATURE COMMUNICATIONS
Volume 12, Issue 1, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41467-021-25411-y
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Funding
- Max Planck Society
- DFG [LE 3260/3-1]
- Graduate School of the Cells-in-Motion Cluster of Excellence [EXC 1003-CiM]
- BMBF [FKZ 031L0127]
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The study compared different CHX-treatment conditions in human cells and yeast, finding that human ribosomes are not affected by CHX and that CHX does not influence the outcome of ribosome profiling experiments in most cases, showing that reported biases of CHX are species-specific.
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.
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