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Genome-wide polysome analysis in poly(I:C)-treated WT and Oasl1-/- BMDM.

ABSTRACT: OASL1 is a novel translation inhibitor for the type I IFN master transcription factor IRF7. To examine whether OASL1 specifically inhibit IRF7 translation, we used a genome-wide gene expression microarray to screen for the polysome-associated mRNAs more enriched in the OASL1 KO BMDMs. The microarray analysis on the polysomal fractions identified 145 candidate transcripts, including IRF7, that showed a signal greater than two-fold higher in poly(I:C)-treated Oasl1-/- BMDM.

ORGANISM(S): Mus musculus

PROVIDER: GSE41787 | GEO | 2013/02/17

SECONDARY ACCESSION(S): PRJNA178176

REPOSITORIES: GEO

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Genome-wide polysome analysis in poly(I:C)-treated WT and Oasl1-/- BMDM.

Project description:OASL1 is a novel translation inhibitor for the type I IFN master transcription factor IRF7. To examine whether OASL1 specifically inhibit IRF7 translation, we used a genome-wide gene expression microarray to screen for the polysome-associated mRNAs more enriched in the OASL1 KO BMDMs. The microarray analysis on the polysomal fractions identified 145 candidate transcripts, including IRF7, that showed a signal greater than two-fold higher in poly(I:C)-treated Oasl1-/- BMDM. We analyzed polysomal fractions from poly(I:C)-treated WT and Oasl1-/- BMDM using the Affymetrix Mouse Gene 1.0 ST array. Array data were processed by Affymetrix GCOS software. We compared these using Affymetrix Expression console1.1, R affy-package(2.9.2), DAVID.

2013-02-17 | E-GEOD-41787 | biostudies-arrayexpress

Arabidopsis polysome microarray

Project description:Microarray experiment with polysomal and non-polysomal RNAs extracted under non-stress and mild-dehydration stress. Keywords = translation Keywords = ribosome loading Keywords = polysome Keywords = dehyrdation Keywords: other

2005-02-12 | GSE2268 | GEO

Polysome profiling RNAseq of cells transfected with an oligonucleotide targeting the ES6S region of the 40S subunit

Project description:Polysome profiling experiments were carried out to identify the mRNAs that have altered the translation efficiency (counts in polysomal fraction/counts in monosomal fractions) in the presence of an oligonucleotide targeting a specific region of the ribosomal RNA, to study the implication of this region in the translation of specific mRNAs

2019-12-10 | GSE129651 | GEO

gcn2/WT polysome loading and transcript level in Arabidopsis thaliana

Project description:To understand the role of GCN2 in regulating translation, we compared the polysome loading state and overall transcript level between Arabidopsis thaliana wild type (ecotype Landsberg erecta) and gcn2 (Genetrap line GT8359, Cold Spring Harbor Laboratory) seedlings with or without herbicide chlorosufuron treatment RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.

2015-12-01 | GSE52116 | GEO

Polysome-profiling of IL4 or INFG polarized BMDMs

Project description:BMDMs from naïve female FVB mice were used to generate BMDMs which were polarized for 4 hours using either INFG or IL4. These were subjected to polysome-profiling.

2021-04-10 | GSE153060 | GEO

Polysome-seq in zebrafish early embryonic development

Project description:We followed the polysomal association of maternal and early zygotic transcriptome over the first few hours of embryonic development, prior to and after MBT. We isolated polysome-associated (bound) and non-polysome-associated (unbound) mRNAs using sucrose gradient centrifugation followed by size fractionation. Using next generation sequencing (RNA-seq), we profiled the transcriptome in polysome-bound and unbound fractions. Our analysis revealed distinct dynamics of polysome association of cytoplasmically polyadenylated maternal mRNAs.

2017-10-14 | GSE88776 | GEO

Changes in polysome association of mRNA throughout growth and development in Arabidopsis thaliana (Polysome association)

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. Experiment using two-flactionated mRNA in 4 developmental stages, Polysomal mRNA vs. total mRNA. Biological replicates: 2. Compared 2DAG and 21DAG, or Young leaves and Mature leaves.

2015-09-01 | E-GEOD-69069 | biostudies-arrayexpress

eif3h/WT polysome loading

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

mouse M-BMDM of WT and STAT2 T403A

Project description:Bone marrow cells were isolated from wild type mouse (WT) or STAT T403A mutant mouse (T403A) and primed with M-CSF (M BMDM) separately. The difference between these two M-BMDMs were distinguished by RNA-seq analysis.

2022-10-31 | GSE179591 | GEO

Transcriptome wide analysis of translation efficiency in MCF7 cells using polysome profiling with and without eIF4A inhibition by hippuristanol treatment

Project description:To identify mRNAs that are most translationally repressed following eIF4A inhibition and those that are relatively insensitive, polysome profiling was carried with and without eIF4A inhibition by hippuristanol treatment. Polysomal, sub-polysomal and total RNA was sequenced and we used a Bayesian model to identify mRNAs that with greatest confidence had shifted from the polysomal into the sub-polysomal fractions, from the sub-polysomal into the polysomal fractionsand those mRNAs that did not change in their polysomal to sub-polysomal ratio, following hipp treatment, which were termed eIF4A-dependent, eIF4A-antidependent and eIF4A-independent mRNAs respectively

2019-11-21 | GSE134888 | GEO

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