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

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

PROVIDER: PRJNA564089 | ENA |

REPOSITORIES: ENA

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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

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

Project description: Not available

| S-EPMC8384890 | biostudies-literature

Cycloheximide can distort measurements of mRNA levels and translation efficiency

Project description:Regulation of the efficiency with which an mRNA is translated into proteins represents a key mechanism for controlling gene expression. Such regulation impacts the number of actively translating ribosomes per mRNA molecule, referred to as translation efficiency (TE), which can be monitored using ribosome profiling and RNA-seq, or by evaluating the position of an mRNA in a polysome gradient. Here we show that in budding yeast, under nutrient limiting conditions, the commonly used translation inhibitor cycloheximide induces rapid transcriptional upregulation of hundreds of genes involved in ribosome biogenesis. Cycloheximide also prevents translation of these newly transcribed messages, leading to an apparent drop in TE of these genes under conditions that include key transitions of the yeast metabolic cycle, meiosis, and amino acid starvation; an effect which is abolished when cycloheximide pretreatment is omitted. This response requires TORC1 signaling, and is modulated by the genetic background as well as the vehicle used to deliver the drug. The present work highlights an important caveat to the use of translation inhibitors when measuring TE, and will hopefully aid in future experimental design as well as interpretation of prior results

2019-03-08 | GSE125038 | GEO

Ribosome profiling data of HEK293T cells treated with C13-benzamidyl cycloheximide

Project description:We performed ribosome profiling in HEK293T cells with treatment with either C13-benzamidyl cycloheximide (hereafter "benzamide") or cycloheximide.

2021-09-28 | GSE184519 | GEO

Expression data from Murine T cell in response to cycloheximide treatment

Project description:Cycloheximide has been used for inhibiting protein synthesis in order to identify IL-2 direct targeted genes in T cells, but the effects of cycloheximide itself on genomewide genes are not well defined We conducted a global analysis of cycloheximide regulated genes in mouse T cell line CTLL-2 using Affymetrix mouse genome array, and identified 213 genes differentially expressed (?1.5-fold change) in response to cycloheximide 30min after adding cylcoheximide to T cells cultured without IL-2 for 14 hours. These genes involve in a number biological processes. Keywords: stress response

2009-01-10 | GSE6084 | GEO

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

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

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Serum stimulation of fibroblasts with cycloheximide

Project description:The transcriptional program in the response of human fibroblasts to serum. Serum was added to fibroblasts in the presence of cycloheximide. This study is described more fully in Iyer VR, et al. 1999. Science 283:83-7 Keywords: time-course

2002-06-27 | GSE56 | GEO

Genomic characterization of five commonly used endometrial cancer cell lines

Project description:Genomic characterization of five commonly used endometrial cancer cell lines

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RNA-seq of 675 commonly used human cancer cell lines

Project description:Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic response1. Although substantial effort has been directed to defining the genomic constitution of cancer cell line panels24, the transcriptome which represents the active program of a cell remains understudied. Here, we describe RNA sequencing and SNP array analysis of 675 commonly used human cancer cell lines. We explore numerous transcriptome features including coding and non-coding gene expression, transcribed mutations, gene fusion and expression of non-human sequences. Aside from many known aberrations we find new surprising characteristics, including more than 2200 unique fusion gene pairs representing a vast, testable repertoire of oncogenic fusions, many of which have analogs found in primary human tumors. We show that a combination of multiple genome and transcriptome features in a novel pathway-based approach enhances prediction of response to various targeted therapeutics. Our results provide valuable new insights into these critical pre-clinical models and provide added context for interpreting the numerous studies that employ these widely used cell lines. The raw sequence files were submitted to the European Genome-Phenome Archive (EGA) under accession EGAS00001000610 ( https://www.ebi.ac.uk/ega/datasets/EGAD00001000725 ). Processed, human non-identifiable data, together with a README file describing the data (140625_Klijn_README.txt) are available here in E-MTAB-2706.additional.*.zip files: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2706/files .

2014-11-25 | E-MTAB-2706 | biostudies-arrayexpress

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

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