PSN1 Polysome and INK128
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE48098 | GEO | 2014/02/03
SECONDARY ACCESSION(S): PRJNA208930
REPOSITORIES: GEO
Similar Datasets
Project description:Polysome-bound mRNA was analyzed to determine the effects of INK128 and radiation on mRNA translation 4 samples were analyzed with 3 biological replicates
2014-02-03 | E-GEOD-48098 | biostudies-arrayexpress
Project description:Hepatitis C Virus protein NS5A was found to upregulate assembly of cap binding initiation complex eIF4F in Huh7.5 cells. NS5A also was found to associate with translation machinery. To understand consequences of NS5A mediation in host translation, we analyzed mRNA associated with polysome fractions of NS5A expressing Huh7.5 cells and compared them with the corresponding fractions from control cells.
2014-05-01 | GSE46273 | GEO
Project description:Oocyte maturation, fertilization, and early embryonic development occur in the absence of gene transcription. Therefore, it is critical to understand at a global level the post-transcriptional events that are driving these transitions. Here, we have used a systems approach by combining polysome mRNA profiling and bioinformatics to identify RNA binding motifs in mRNAs that either enter or exit the polysome pool during mouse oocyte maturation. Association of mRNA with the polysomes correlates with active translation. Forty-eight hours (h) after PMSG injection, mice were stimulated with hCG for 0, 4, or 14 h, and GV-, MI- and MII-stage oocytes were collected. Polysome-bound mRNAs were purified, reverse-transcribed and linearly amplified with the WT-Ovation FFPE RNA Amplification System V2 (NuGEN). 5µg cDNA were fragmented and hybridized with Affymetrix Mouse Genome 430.2 array chips. Experiments were done using 3 independent sample sets.
2012-01-14 | E-GEOD-35106 | biostudies-arrayexpress
Project description:Although ionizing radiation has been shown to influence gene transcription, little is known about the effects of radiation on gene translational efficiency. To obtain a genome-wide perspective of the effects of radiation on gene translation, microarray analysis was done on polysome-bound RNA isolated from irradiated human brain tumor cells; to allow for a comparison with the effects of radiation on transcription, microarray analysis was also done using total RNA. The number of genes whose translational activity was modified by radiation was f10-fold greater than those whose transcription was affected. The radiation-induced change in a gene’s translational activity was shown to involve the recruitment of existing mRNAs to and away from polysomes. Moreover, the change in a gene’s translational activity after irradiation correlated with changes in the level of its corresponding protein. These data suggest that radiation modifies gene expression primarily at the level of translation. In contrast to transcriptional changes, there was considerable overlap in the genes affected at the translational level among brain tumor cell lines and normal astrocytes. Thus, the radiation-induced translational control of a subset of mRNAs seems to be a fundamental component of cellular radioresponse. (Cancer Res 2006; 66(2): 1052-61) There are 32 samples in total in this study. Each sample has a technical duplicate (16samples x2). Comparison of radiation-induced gene expression profiles generated from microarray analysis of total and polysome-bound RNA isolated from three brain tumor cell lines U87, SF126, SF539 and normal astrocytes. Cells were irradiated at the dose of 7gy and collected 6 hours later for isolation of total cellar RNA or polysome-bound RNA. Gene expression was directly compared between irradiated and unirradiated control cells for total and polysome RNA. The array labeling is two-dye method. Labeling two dye samples are labeled using CY3 dye. All the human reference RNA from Stratagene are labeled using CY5 dye.
2008-05-21 | E-GEOD-11517 | biostudies-arrayexpress
Project description:Microarray comparisons of polysome loading in wild-type Arabidopsis and eif3h mutant Goal: To find the target mRNAs that are translationally regulated by eIF3h. BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. RESULTS: Working with stable reporter transgenes in Arabidopsis thaliana it was demonstrated that the h subunit of eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5’ leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Microarray comparisons of polysome loading in wild-type and eif3h mutant plants revealed that eIF3h generally helps to maintain efficient polysome loading of mRNAs harboring multiple uORFs. Independently, eIF3h also boosted polysome loading of mRNAs with long coding sequences. Moreover, the lesion in eIF3h revealed a concerted upregulation of translation for specific functional subgroups of mRNAs, including ribosomal proteins and proteins involved in photosynthesis. CONCLUSIONS: The intact eIF3h protein contributes to efficient translation initiation on 5’ leader sequences harboring multiple uORFs, although mRNA features independent of uORFs were also implicated. Moreover, our data suggest that regulons of translational control can be revealed by mutations in generic translation initiation factors. Keywords: mutant, polysome, non-polysome
2007-05-01 | GSE6024 | GEO
Project description:Transcriptional profiling of Cytoplasmic mRNA and Heavy polysome-associated mRNAs extracted from U251 Cells treated with control siRNA or siRNA targeting eIF3e . Goal was to determine the effect of eIF3e knockdown on translation of specific mRNAs.
2020-09-09 | GSE157608 | GEO
Project description:Translational control is a key regulatory step in the expression of genes as proteins. In plant cells, translational efficiency of mRNAs differs on different mRNA species, and the efficiency dynamically changes in various conditions. To gain a global view of translational control throughout growth and development, we performed genome-wide analysis of polysome association of mRNA over growth and leaf development in Arabidopsis thaliana by applying the mRNAs in polysome to DNA microarray. This analysis revealed that the degree of polysome association of mRNA had different levels depending on mRNA species, and the polysome association changed greatly throughout growth and development for each. In the growth stage, transcripts showed varying changes in polysome association from strongly depressed to unchanged degree, with the majority of transcripts showing dissociation from ribosomes. On the other hand, during leaf development, the polysome association of transcripts showed a normal distribution from repressed to activated mRNAs when comparing between expanding and expanded leaves. In addition, functional category analysis of the microarray data suggested that translational control has a physiological significance in plant growth and development process, especially in category of signaling and protein synthesis. Besides this, we compared changes in polysome association of mRNAs between various conditions and characterized translational controls in each. This result suggested that mRNAs translation might be controlled by complicated mechanisms for response to each condition. Our results highlight the importance of dynamic changes in mRNA translation in plant development and growth.
2015-09-01 | GSE69069 | GEO
Project description:Analysis of gene expression level. The hypothesis tested in the present study was that rea1 mutant influence the translation level of translation and nucleosome assembly associated genes. Results provide important information of the gene translation level regulation of ribosome proteins, elongation factors, histones and genes associated with other biological processes. Endosperm total and polysome-bound mRNA profiles of 15DAP wild type (WT) and rea1 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).
2015-04-25 | E-GEOD-67083 | biostudies-arrayexpress
Project description:We use mRNA-seq in combination with polysome profiling to determine translational status for all mRNAs in Drosophila mature oocytes and activated eggs. Puromycin-treated lysates are used as a negative control in polysome profiling experiments. Additionally, we use ribosome footprinting to globally measure translational efficiency of mRNAs in wild type mature oocytes as well as wild type and png mutant activated eggs. Lysates of hand-dissected Drosophila mature oocytes (containing ~540 M-NM-<g of total RNA) were subjected to separation by velocity sedimentation through sucrose gradients. In this way, free mRNAs (present in RNPs fraction) or those comigrating with ribosomal subunits (40S or 60S+80S fractions) or with varying numbers of bound ribosomes (low polysomes (2-4 ribosomes), medium polysomes (5-9 ribosomes), and heavy polysomes (more than 10 ribosomes) can be separated based on their size and collected as sucrose gradient fractions. To compare quantitatively the levels of every mRNA across the polysome gradient fractions, we added 5ng of S. cerevisiae mRNA as an exogenous spike-in to each of the six fractions of interest: RNPs, 40S, 60S+80S, low polysomes, medium polysomes and heavy polysomes. RNA was extraced from these fractions, follwing proteinase K treatment, by hot acid phenol method. In case of unfractionated lysates, RNA was extracted using TRIzol (Invitrogen) according to manufacturerM-bM-^@M-^Ys instructions. mRNA-seq samples were prepared from 1 M-NM-<g of total RNA (in case of sucrose gradient fractions and unfractionated lysates) and subject to Illumina based sequencing. Puromycin-treated lysates of mature oocytes or 0-2h Drosophila activated eggs (containing ~540 M-NM-<g of total RNA) were also subjected to separation by velocity sedimentation through sucrose gradients. Puromycin causes premature termination of elongating ribosomes and thus it can be used to determine whether the mRNAs co-sedimenting with the polysomal peaks (defined here as M-bM-^IM-%5 ribosomes) were actively engaged in translation. As an independent approach to assess translation and obtain information on the position of ribosomes on mRNAs, we employed ribosome footprinting. In addition to analyzing the same samples, as by polysome profiling, we also analyzed png mutant activated eggs by ribosome footprinting. Ribosome footprint profiling measures the number of ribosome-protected fragments (RPFs) derived from the mRNAs of each gene, resulting in a singular value of translational efficiency (TE) for each gene (TE=RPF/RNA).
2014-06-12 | E-GEOD-52799 | biostudies-arrayexpress
Project description:Using platinum-resistant OVCAR-3 cells treated with the selective mTORC1/2 inhibitor INK128/MLN128, we conducted genome-wide transcription and translation studies and analyzed the effect on cell proliferation, AKT-mTOR signaling and cell survival, to determine whether carboplatin resistance involves selective mRNA translational reprogramming, and whether it is sensitive to mTORC1/2 inhibitio.n
2018-07-31 | GSE116387 | GEO