Transcriptomics

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Time resolved ribosome profiling study of oxygen and glucose deprivation of rat pheochromocytoma cells


ABSTRACT: Oxygen and glucose metabolism plays a pivotal role in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) occurs during ischemia and stroke, resulting in extensive tissue injury and cell death. We applied time-resolved ribosome profiling technique to assess early events at the level of gene expression in rat pheochromocytoma PC12 cells during short-term OGD. Most substantial alterations in transcripts levels and their translation were seen to occur in the first 20 minutes of OGD. The rapid adaptation of translation apparatus to OGD is global and involves altered elongation and initiation rates. We also observed salient and reproducible alterations in ribosome densities of individual mRNAs such as increased translation of particular upstream Open Reading Frames (uORFs); induced site-specific arrests of the ribosomes and synthesis of extended protein isoforms. Ribosome profiling (with mRNA-seq sequencing) was carried out at 0,20,40 and 60 minutes of OGD. Two biological replicates were used.

ORGANISM(S): Rattus norvegicus  

SUBMITTER: Alexander V Zhdanov  Ivan N Shatsky   Dmitry E Andreev   Patrick B O’Connor   Ruslan I Dmitriev   Dmitry B Papkovsky   Pavel V Baranov    

PROVIDER: E-GEOD-60752 | ArrayExpress | 2015-04-10

SECONDARY ACCESSION(S): SRP045777GSE60752PRJNA259424

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes.

Andreev Dmitry E DE   O'Connor Patrick B F PB   Zhdanov Alexander V AV   Dmitriev Ruslan I RI   Shatsky Ivan N IN   Papkovsky Dmitri B DB   Baranov Pavel V PV  

Genome biology 20150506


Oxygen and glucose metabolism play pivotal roles in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) during ischemia and stroke results in extensive tissue injury and cell death.Using time-resolved ribosome profiling, we assess gene expression levels in a neural cell line, PC12, during the first hour of OGD. The most substantial alterations are seen to occur within the first 20 minutes of OGD. While transcription of only 100 genes is significantly altered  ...[more]

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