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

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

PROVIDER: PRJNA764910 | ENA |

REPOSITORIES: ENA

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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.

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Ribosome profiling in transgenic and HEK293T cells treated with NAEK

Project description:To investigate whether natural TAG was decoded by stably transfected Mb pyltRNA in transgenic cells, their cell lysate was subjected to ribosome profiling, examining the physical locations of ribosomes. HEK293T cells were taken as control.

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Project description:To investigate whether natural TAG can be decoded by stably transfected pyltRNA, whole cell lysate of transgenic cells was collected 48h after the addition of NAEK and subjected to ribosome profiling, examining the physical locations of ribosomes along 15662 TAG terminated transcripts. And HEK293T cells were taken as control.

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

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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

Ribosome profiling of Tunicamycin-treated and -untreated 17Cl1 cells

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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

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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

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