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Oxygen-dependent translation efficiency (TE) and mRNA expression analysis

ABSTRACT: Oxygen-dependent translation efficiency (TE) and mRNA expression analysis

PROVIDER: PRJNA528083 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8753644.fastq.gz	Fastqsanger.gz
	SRR8753645.fastq.gz	Fastqsanger.gz
	SRR8753646.fastq.gz	Fastqsanger.gz
	SRR8753647.fastq.gz	Fastqsanger.gz
	SRR8753648.fastq.gz	Fastqsanger.gz

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Oxygen-dependent translation efficiency (TE) and mRNA expression analysis

Project description:mRNA TE and steady-state levels were measured in U87MG cells subjected to 21% or 1% oxygen followed by ribosome density fractionation.

2020-04-23 | GSE128547 | GEO

Hypoxia-Acidosis translation efficiency (TE) and mRNA expression analysis

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HuR-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

Project description:HuR-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

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HIF-2α- and HIF-1α-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

Project description:HIF-2α- and HIF-1α-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

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HuR-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

Project description:mRNA TE and steady-state levels were measured in hypoxic U87MG cells treated with non-silencing control or HuR-specific siRNA pools followed by ribosome density fractionation.

2020-04-23 | GSE128541 | GEO

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

Hypoxia-Acidosis translation efficiency (TE) and mRNA expression analysis

Project description:mRNA TE and steady-state levels were measured in normoxic, normoxia-acidosis, hypoxia, hypoxia acidosis U87MG from RNA seq of ribosome density fractionation.

2020-04-23 | GSE139233 | GEO

HIF-2α- and HIF-1α-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

Project description:mRNA TE and steady-state levels were measured in hypoxic U87MG cells treated with non-silencing control or HIF-2α-specific or HIF-1α-specific siRNA pools followed by ribosome density fractionation.

2020-04-23 | GSE128555 | GEO

Systemic remodeling of translation efficiencies on oxygen stimulus.

Project description:Protein concentrations evolve under greater evolutionary constraint than mRNA levels. In addition, translation efficiency of mRNA populations represents the chief determinant of basal protein concentrations. This raises a fundamental question as to how mRNA and protein levels are actively coordinated in dynamic systems responding to acute physiological stimuli. This report examines the contributions of mRNA abundance and translation efficiency to protein output in cells responding to oxygen stimulus. We show that alternative translation efficiencies, not mRNA levels, represent the major adaptive mechanism that governs the cellular response to perturbations in [O2]. This phenomenon is coordinated by eIF4F under atmospheric [O2] and the previously uncharacterized hypoxic eIF4F (eIF4FH) under low [O2]. The oxygen-regulated remodeling of translation efficiency enables oxygenated and hypoxic cells to produce surprisingly divergent translatomes of similar complexity, with minimal dependence on mRNA levels. Changes in mRNA concentrations observed between normoxic and hypoxic cells are likely neutral, as they are during evolution. We propose that mRNAs contain hard-wired translation efficiency determinants for their triage by the translation apparatus on [O2] stimulus.

2016-07-20 | MSV000079962 | MassIVE

PABPN1 effect on translation efficiency.

Project description:PABPN1 effect on translation efficiency.

| PRJNA695208 | ENA