Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide analysis of eIF4G-RNA interaction in CDK12-depleted cells (Ribo-Seq)

ABSTRACT: Methods: U2OS mRNA profiles of control siRNA(siControl) and siCDK12 were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level. Total RNA-Seq was used for normalzation of RIP-Seq signals.Results: We report the application of RNA-immunoprecipitation-based sequencing for high-throughput profiling of mRNA abundence in mammalian cells. We generated genome-wide views of translation rate in CDK12-depleted U2OS cells in comparion to mTOR inhibitor, rapamycin treatment. We find that significant overlap and high corelation of change in eIF4G-associated mRNAs between two condition, rapamycin treatment and siCDK12 transfected cells. This study provides a role of CDK12 in translation control of mammalian cell.

ORGANISM(S): Homo sapiens

PROVIDER: GSE121391 | GEO | 2019/06/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide analysis of eIF4G-RNA interaction in CDK12-depleted cells (RIP-Seq)

Project description:Methods: U2OS mRNA profiles of control siRNA(siControl) and siCDK12 were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level. Total RNA-Seq was used for normalzation of RIP-Seq signals. Results: We report the application of RNA-immunoprecipitation-based sequencing for high-throughput profiling of mRNA abundence in mammalian cells. We generated genome-wide views of translation rate in CDK12-depleted U2OS cells in comparion to mTOR inhibitor, rapamycin treatment. We find that significant overlap and high corelation of change in eIF4G-associated mRNAs between two condition, rapamycin treatment and siCDK12 transfected cells. This study provides a role of CDK12 in translation control of mammalian cell.

2019-06-12 | GSE121390 | GEO

Yeast eIF4G homogenic whole cell oxidative stress LC-MSMS

Project description:Translation initiation factor 4G (eIF4G) is an integral component of the eIF4F complex which is key to translation initiation for most eukaryotic mRNAs. Many eIF4G isoforms have been described in diverse eukaryotic organisms but we currently have a poor understanding of their functional roles and whether they regulate translation in an mRNA specific manner. The yeast Saccharomyces cerevisiae expresses two eIF4G isoforms, eIF4G1 and eIF4G2, that have previously been considered as functionally redundant with any phenotypic differences arising due to alteration in eIF4G expression levels. Using homogenic strains that express eIF4G1 or eIF4G2 as the sole eIF4G isoforms at comparable expression levels to total eIF4G, we show that eIF4G1 is specifically required to mediate the translational response to oxidative stress. We use quantitative proteomics to show that eIF4G1 promotes oxidative stress-specific proteome changes.

2023-10-24 | PXD041682 | Pride

Transcription profiling of Saccharomyces cerevisiae eIF4G isoforms to investigate eIF4G deletion transcript abundance

Project description:Effect of eIF4G gene deletion on transcript abundance.

2009-10-24 | E-MEXP-2400 | biostudies-arrayexpress

Transcription profiling of Saccharomyces cerevisiae eIF4G isoforms to investigate eIF4G deletion ribosome occupancy

Project description:Effect of eIF4G gene deletion on the ribosome occupancy.

2009-10-24 | E-MEXP-2399 | biostudies-arrayexpress

Genome-wide analysis of eIF4G-RNA interaction in CDK12-depleted cells

Project description:Genome-wide analysis of eIF4G-RNA interaction in CDK12-depleted cells

| PRJNA497249 | ENA

Transcription profiling of Saccharomyces cerevisiae eIF4G isoforms to investigate eIF4G homogenic polysome abundance

Project description:Effect of expressing a single eIF4G isoform at wild type levels on relative polysome abundance.

2009-10-14 | E-MEXP-2402 | biostudies-arrayexpress

Lifespan extension via eIF4G inhibition is mediated by post-transcriptional remodeling of stress response gene expression in C. elegans

2011-04-16 | GSE28665 | GEO

Lifespan extension via eIF4G inhibition is mediated by post-transcriptional remodeling of stress response gene expression in C. elegans

Project description:Reducing protein synthesis slows growth and development but can increase adult lifespan. We demonstrate that knock-down of eukaryotic translation initiation factor 4G (eIF4G), which is down-regulated during starvation, results in differential translation of genes important for growth and longevity in C. elegans. Genome-wide mRNA translation state analysis showed that inhibition of IFG-1, the C. elegans ortholog of eIF4G, results in a relative increase in ribosomal loading and translation of stress response genes. Some of these genes are required for lifespan extension when IFG-1 is inhibited and are new determinants of longevity. Furthermore, enhanced ribosomal loading of certain mRNAs upon IFG-1 inhibition was correlated with increased mRNA length. This association was supported by changes in the proteome assayed via quantitative mass spectrometry. Our results support a role for IFG-1 in mediating the antagonistic effects on growth and somatic maintenance by modulating translation of a specific class of mRNA based on transcript length. 24 experimental samples were analyzed using custom oligo microarrays. A wild type sample pool was used as the Cy3 reference/control for all experimetal samples. All extracted RNA prior to array analysis was fractioned (via a sucrose gradient) based on ribosomal loading and pooled into ribosomal and free RNA (Fraction1), light polysomes (Fraction2) and heavy polysomes (Fraction3) as described in the experimental procedures. The control RNAi is ‘empty’ vector L4440 RNAi feeding vector plasmid (1999 Firelab vector kit) transformed HT115(DE3), which was obtained from the Caenorhabditis Genetics Center (University of Wisconsin).

2011-04-16 | E-GEOD-28665 | biostudies-arrayexpress

Genome-wide analysis of eIF4G-RNA interaction in CDK12-depleted cells (RIP-Seq)

Project description:Genome-wide analysis of eIF4G-RNA interaction in CDK12-depleted cells (RIP-Seq)

| PRJNA497254 | ENA

Genome-wide analysis of eIF4G-RNA interaction in CDK12-depleted cells (Ribo-Seq)

Project description:Genome-wide analysis of eIF4G-RNA interaction in CDK12-depleted cells (Ribo-Seq)

| PRJNA497255 | ENA