Andreev et al. 2015 (PRJNA259424)

General Details

Title Time resolved ribosome profiling study of oxygen and glucose deprivation of rat pheochromocytoma cells
Organism
Number of Samples 8
Release Date 2014/08/26 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP045777
ENA SRP045777
GEO
BioProject PRJNA259424

Publication

Title
Authors Andreev DE,O'Connor PB,Zhdanov AV,Dmitriev RI,Shatsky IN,Papkovsky DB,Baranov PV
Journal Genome biology
Publication Date 2015 May 6
Abstract 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 during one hour of OGD, the translation response affects approximately 3,000 genes. This response involves reprogramming of initiation and elongation rates, as well as the stringency of start codon recognition. Genes involved in oxidative phosphorylation are most affected. Detailed analysis of ribosome profiles reveals salient alterations of ribosome densities on individual mRNAs. The mRNA-specific alterations include increased translation of upstream open reading frames, site-specific ribosome pauses, and production of alternative protein isoforms with amino-terminal extensions. Detailed analysis of ribosomal profiles also reveals six mRNAs with translated ORFs occurring downstream of annotated coding regions and two examples of dual coding mRNAs, where two protein products are translated from the same long segment of mRNA, but in two different frames. These findings uncover novel regulatory mechanisms of translational response to OGD in mammalian cells that are different from the classical pathways such as hypoxia inducible factor (HIF) signaling, while also revealing sophisticated organization of protein coding information in certain genes.
PMC PMC4419486
PMID 25943107
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR1557705 PRJNA259424 Rattus norvegicus PC12 Ribo-Seq
SRR1557707 PRJNA259424 Rattus norvegicus PC12 Ribo-Seq
SRR1557709 PRJNA259424 Rattus norvegicus PC12 Ribo-Seq
SRR1557711 PRJNA259424 Rattus norvegicus PC12 Ribo-Seq
SRR1557713 PRJNA259424 Rattus norvegicus PC12 Ribo-Seq
SRR1557715 PRJNA259424 Rattus norvegicus PC12 Ribo-Seq
SRR1557717 PRJNA259424 Rattus norvegicus PC12 Ribo-Seq
SRR1557719 PRJNA259424 Rattus norvegicus PC12 Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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