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PAB/WT polysome loading and transcript levels (Arabidopsis thaliana)

ABSTRACT: To understand the contribution of the poly(A)binding protein to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and pab2 pab8 double mutant seedlings. The mutants continue to express the PAB4 paralog of PABP. RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE51480 | GEO | 2014/01/01

SECONDARY ACCESSION(S): PRJNA223278

REPOSITORIES: GEO

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PAB/WT polysome loading and transcript levels (Arabidopsis thaliana)

Project description:To understand the contribution of the poly(A)binding protein to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and pab2 pab8 double mutant seedlings. The mutants continue to express the PAB4 paralog of PABP. RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays. Each plant sample was analyzed for the mRNA abundance in total mRNA (T), polysomal mRNA (PL), and nonpolysomal mRNA (NP). Four biological replicates were collected for polysomes and three for total RNA. The pab2 pab8 double mutant was compared with wild type.

2014-01-01 | E-GEOD-51480 | biostudies-arrayexpress

rpl24b/WT polysome loading and transcript levels (Arabidopsis thaliana)

2014-01-01 | GSE51474 | GEO

rpl24b/WT polysome loading and transcript levels (Arabidopsis thaliana)

Project description:To understand the contribution of the RPL24B protein, a component of the large 60S ribosomal subunit, to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and the rpl24b/stv1-1 T-DNA insertion mutant. RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays. Each plant sample was analyzed for the mRNA abundance in total mRNA, polysomal mRNA, and nonpolysomal mRNA. Three biological replicates were collected. The rpl24b mutant was compared with wild type.

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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

Response to herbicide treatment in wild type and gcn2 at the transcription and translation level in Arabidopsis thaliana

Project description:To understand the role of GCN2 in stress response, the total transcript and translation state were compared 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 | GSE52117 | GEO

eif3k/WT polysome loading

Project description:To understand the contribution of the k subunit of eukaryotic transcription factor 3 (eif3k) to the translation of specific mRNAs, we compared the polysome loading states and overall transcript levels of wild type Arabidopsis and the eif3k T-DNA insertion mutant by Affymetrix arrays. We analyzed the polysome loading states of wild type Arabidopsis and the eif3k mutant using the Arabidopsis Affymetrix ATH1 array. Data from 3 biological replicates were collected.

2011-03-29 | E-GEOD-28223 | biostudies-arrayexpress

Translational activation of developmental mRNAs during neonatal mouse testis development

Project description:The sequence of gene regulatory events that drive neonatal germ cell development in the mammalian testis is not yet clear. We assessed changes in mRNA utilization in the neonatal testis at 1 and 4 dpp, times when the testis contains quiescent gonocytes (1 dpp) and proliferating spermatogonia (4 dpp). There are not thought to be major changes in the nature or number of somatic cells over that interval. We used microarrays to detail the global expression levels of mRNA distribution between non-translating mRNAs and efficiently translating mRNAs during testis development at 1 dpp and 4 dpp Extracts of mouse testes from 1 dpp and 4 dpp CD-1 mice were fractionated over a sucrose gradient in triplicate. Gradients were fractionated using an ISCO gradient fractionation system equipped with a UA-6 detector. The position of the 80S peak defined the boundary between translating and non-translating mRNAs. Pooled non-polysomal (non-translating; fractions 1-3) and heavy polysomal (efficiently translating, fractions 7-13) RNAs were isolated from sucrose gradient fractions for hybridization on Affymetrix 420 2.0 microarrays.

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Temporally-regulated tRNA-derived small RNAs are associated primarily with non-polysomal fractions in Drosophila

Project description:Eukaryotic genomes contain various types of small non-coding RNAs such as microRNAs (miRNAs), silencing RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). Recent studies point to the presence of a more diverse array of uncharacterized small regulatory RNAs including those that are generated from mRNAs, rRNAs and tRNAs. To explore the possible involvement of tRNA-derived fragments (tRFs) in translational regulation, we fractionated 1 and 8h Drosophila embryos on sucrose density gradients and quantitatively measured by deep-dequencing the expression levels of the tRFs in the fractionated and unfractionated Drosophila embryonic cytosolic extracts. Analysis of 9,007,661 reads has revealed that tRFs, which are produced mainly from the 5’ends of a subset of tRNAs, are mostly associated with the non-polysomal fractions in Drosophila embryos. Quantitative analysis indicates that the expression levels of a subset of tRFs change temporally following the maternal-tozygotic transition in embryos. We detected non-polysomal association of tRFs in S2 cells as well. When transfected into S2 cells, the biotinylated tRFgly:GCC:5 co-fractionated with the non-polysomal complexes similar to the endogenous tRFgly:GCC:5 in embryos and S2 cells. These results suggest that the tRFs, which are much smaller in size than the stres-induced tRNA fragments, are generated selectively from a fraction of tRNAs and that they associate primarily with the non-polysomal complexes in Drosophila embryos and S2 cells.

2018-02-12 | GSE35443 | GEO

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

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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