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Effects of cycloheximide (CHX) on ribosome profiling experiments in Schizosaccharomyces pombe

ABSTRACT: Effects of cycloheximide (CHX) on ribosome profiling experiments in Schizosaccharomyces pombe

PROVIDER: PRJEB21099 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1994960.fastq.gz	Fastqsanger.gz
	ERR1994970.fastq.gz	Fastqsanger.gz
	ERR1994961.fastq.gz	Fastqsanger.gz
	ERR1994971.fastq.gz	Fastqsanger.gz
	ERR1994962.fastq.gz	Fastqsanger.gz

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Effects of cycloheximide (CHX) on ribosome profiling experiments in Schizosaccharomyces pombe

Project description:CHX is an inhibitor of translation elongation often used in ribosome profiling experiments. There is evidence that CHX treatment of cells may cause artefacts in the distribution of ribosomes on mRNAs. We investigate this possibility in S. pombe by performing ribosome profiling in the presence and absence of this drug.

2017-09-05 | E-MTAB-5794 | biostudies-arrayexpress

Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

Project description: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.

2021-07-28 | GSE136940 | GEO

Nascent Transcriptome of Cycloheximide (CHX)-arrested Xenopus laevis Embryos from 5-7.5 hpf

Project description:To characterize the effect of cell cyle elongation on nascent transcription during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and treated the embryos with 0.2 mg/ml of cycloheximide (CHX) to arrest them in interphase from 5 hpf to 7.5 hpf. Control and CHX-arrested embryos were collected for isolating total RNAs, followed by biotinylation using disulfide biotin azide via click reaction and purification of nascent transcripts using streptavidin beads. Libraries were constructed and sequenced on illumina NextSeq 500.

2022-08-22 | GSE201834 | GEO

Cellular responses to long-term phosphate starvation of fission yeast: Maf1 determines fate choice between quiescence and death associated with aberrant tRNA biogenesis (CHX experiments)

Project description:This RNA-Seq analysis compares gene expression of fission yeast cells (Schizosaccharomyces pombe) at various times after phosphate starvation (2, 4, and 8 HR) either with 100 µg/ml cycloheximide or without drug contrasting to the cells grown in phosphate replete conditions (0HR) in the absence of the drug.

2023-01-19 | GSE217952 | GEO

Effects of cycloheximide on the interpretation of ribosome profiling experiments in Schizosaccharomyces pombe.

Project description:Stress conditions lead to global and gene-specific changes in RNA translation. Ribosome profiling experiments have identified genome-wide alterations in the distribution of ribosomes along mRNAs. However, it is contentious whether these changes reflect real responses, or whether they are artefacts caused by the use of inhibitors of translation (notably cycloheximide). To address this issue we performed ribosome profiling with the fission yeast Schizosaccharomyces pombe under conditions of exponential growth (unstressed) and nitrogen starvation (nutritional stress), and both in the presence and absence of cycloheximide. We examined several aspects of the translational response, including density of ribosomal footprints on coding sequences, 5' leader ribosomal densities, distribution of ribosomes along coding sequences, and ribosome codon occupancies. Cycloheximide had minor effects on overall ribosome density, which affected mostly mRNAs encoding ribosomal proteins. Nitrogen starvation caused an accumulation of ribosomes on 5' leaders in both cycloheximide-treated and untreated cells. By contrast, stress-induced ribosome accumulation on the 5' side of coding sequences was cycloheximide-dependent. Finally, codon occupancy showed strong positive correlations in cycloheximide-treated and untreated cells. Our results demonstrate that cycloheximide does influence some of the results of ribosome profiling experiments, although it is not clear if this effect is always artefactual.

| S-EPMC5583251 | biostudies-literature

α-arrestin-dependent endocytosis after cycloheximide treatment

Project description:To identify new plasma membrane (PM) proteins that require α-arrestins for endocytosis, we performed an iTRAQ-based quantitative proteomic screening. We analysed and compared the PM proteome for each arrestin knockout (art∆) strain to a WT strain after a 90 min cycloheximide (CHX) treatment. CHX is a translation inhibitor and can trigger the endocytosis of several transporters in a substrate-independent manner. We searched for proteins that underwent CHX-induced endocytosis in a WT strain but that remained stabilized at the PM in an art∆ strain.

2019-09-25 | PXD014695 | Pride

Nascent Transcriptome of Cycloheximide (CHX)-arrested Xenopus laevis Embryos from 5-7.5 hpf

Project description:Nascent Transcriptome of Cycloheximide (CHX)-arrested Xenopus laevis Embryos from 5-7.5 hpf

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Analysis of the effect of CHX on the cultured podocyte proteome

Project description:We analyzed the effect of Cycloheximide (CHX) on the podocyte proteome in both the differentiated and undifferentiated state.

2018-05-01 | PXD006886 | Pride

ATAC-seq and H4K16ac ChIP-seq profiles of E14 ES cells treated with cycloheximide

Project description:ATAC-seq and H4K16ac ChIP-seq profiles of E14 ES cells before and after treatment with cycloheximide (CHX, 1 ug/ml) for 3 hours.

2017-07-23 | GSE98358 | GEO

Schizosaccharomyces pombe

Project description:Schizosaccharomyces pombe

| PRJNA239187 | ENA