Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Changes in transcript abundance and association with large polysomes in response to hypoxia stress

ABSTRACT: 7d-old WT ler seedlings were submitted to 12h of non-stress (air) or hypoxia-stress treatment under low light conditions (45 uM m-2 s-2), and Total and Large Polysome RNA from both treatments were extracted and hybridized against Affymetrix genome chips. Values were used to evaluate changes in transcript abundance and transcript association with large polysomal complexes. TABLE 1 - Comparison between transcript abundance in non-stress and hypoxia-stress conditions. TABLE 2 - Comparison between transcript abundance in large polysome complexes (5 or more ribosomes per mRNA) in non-stress and 12 hypoxia-stress conditions. TABLE 3 - Proportion of total transcript that is associated with large polysome complexes (polysome loading) under non-stress conditions. Raw data (not normalized) TABLE 4 - Proportion of total transcript that is associated with large polysome complexes (polysome loading) under 12h of hypoxia-stress. Raw data (not normalized) Keywords: time-course

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE2218 | GEO | 2005/05/31

SECONDARY ACCESSION(S): PRJNA91467

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profiling of Arabidopsis under hypoxia stress to assess proportion of transcript associated with large polysomes

Project description:7d-old WT ler seedlings were submitted to 12h of non-stress (air) or hypoxia-stress treatment under low light conditions (45 uM m-2 s-2), and Total and Large Polysome RNA from both treatments were extracted and hybridized against Affymetrix genome chips. Values were used to evaluate changes in transcript abundance and transcript association with large polysomal complexes. TABLE 1 - Comparison between transcript abundance in non-stress and hypoxia-stress conditions. TABLE 2 - Comparison between transcript abundance in large polysome complexes (5 or more ribosomes per mRNA) in non-stress and 12 hypoxia-stress conditions. TABLE 3 - Proportion of total transcript that is associated with large polysome complexes (polysome loading) under non-stress conditions. Raw data (not normalized); TABLE 4 - Proportion of total transcript that is associated with large polysome complexes (polysome loading) under 12h of hypoxia-stress. Raw data (not normalized)

2008-06-11 | E-GEOD-2218 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Changes in transcript abundance and association with large polysomes in response to hypoxia stress

| PRJNA91467 | ENA

Project description:eif3k/WT polysome loading and transcript levels

| PRJNA139609 | ENA

Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation

Project description:The stability of mRNA is an important determinant of its abundance and, consequently, protein production. There has been extensive research on the pathways governing mRNA stability and translation, however, it is unclear the extent to which these processes are modulated by environmental conditions. We previously modelled rapid recovery gene down-regulation (RRGD) following light stress in Arabidopsis thaliana (Arabidopsis) using mathematical calculations to account for transcription in order to predict half-lives and led to the hypothesis of recovery-specific transcript destabilisation. Here, we test this hypothesis by quantifying changes in transcription, mRNA stability, and translation in leaves of mature Arabidopsis undergoing light stress and recovery and investigate processes regulating transcript abundance and fate. Compared to juvenile plants from prior work, here we find that stability is altered for a range of transcripts that encode proteins involved in post-transcriptional processes in mature leaves. We also observe transcript destabilisation during light stress, followed by re-stabilisation upon recovery. Alongside this, we observe fast transcriptional shut-off in recovery that, when paired with transcript destabilisation, promotes rapid down-regulation of stress-induced genes. Translation was dynamic over the course of light stress and recovery, with substantial transcript-specific increases in polysome loading observed during late stress independently of total mRNA abundance. Taken together, we provide evidence for the combinatorial regulation of transcription, mRNA stability, and translation that occurs during light stress and recovery.

2022-06-10 | GSE201015 | GEO

E-GEOD-51480

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

2015-12-04 | E-GEOD-51480 | ExpressionAtlas

Ethylene modulates the dynamics of translation via GCN2 and EIN2 in Arabidopsis under submergence

Project description:General translational repression is predicted as a key process to reduce energy consumption under hypoxia. We have previously showed that mRNA loading onto polysome is reduced in Arabidopsis under submergence. Here, we showed that plant stress activated GCN2 (general control nonderepressible 2) can phosphorylate eIF2a (Eukaryotic Initiation Factor 2a) in Arabidopsis under submergence, and this process is reversible after desubmergence. Compared to the wild-type, the reduction in polysome loading during submergence was less severe in the gcn2 mutant. Transgenic lines overexpressing GCN2 had more ATP and conferred better tolerance under submergence, suggesting that GCN2 might modulate the dynamics of translation to adjust the energy homeostasis under hypoxia. Interestingly, GCN2-eIF2a signaling was activated by ethylene under submergence. However, GCN2 activity was not affected in ein2-5 and eil1ein3 under submergence, suggesting that GCN2 activity was regulated by noncanonical ethylene signaling. In addition, the polysome loading was retained in both ein2-5 and etr1-1 under submergence, implying that ethylene modulated the dynamic translation under submergence via EIN2 and GCN2. Notably, our NGS analysis also demonstrated that EIN2 and GCN2 regulated the translation of 23 core hypoxia genes as well as 53% translational repressed genes under submergence. On the other hand, EIN2 and GCN2 also affected the expression of genes involved in hypoxic response, ethylene response, biotic stress and negative regulation of cytokinin signaling. Taken together, these demonstrated that entrapped ethylene triggers GCN2 and EIN2 to ensure the translation of stress required proteins under submergence and also provide a step stone for future investigation how eukaryotic cells modulate the translation to response for the changeable environments.

2022-06-08 | GSE149414 | GEO

Arabidopsis thaliana

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

| PRJNA223278 | ENA

Arabidopsis thaliana

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

| PRJNA223281 | ENA

Transcription profiling of mouse embryonic stem cells (ESCs) differentiation into embyroid bodies (EBs

Project description:Stem cell differentiation is known to involve changes in RNA expression, but little is known about translational control during differentiation. We comprehensively profiled gene expression during differentiation of embryonic stem cells (ESCs) into embyroid bodies (EBs) by integrating conventional transcriptome analysis with global assessment of ribosome loading. Differentiation was accompanied by an anabolic switch, characterized by global increases in transcript abundance, polysome content, protein synthesis rates and protein content. Furthermore, 78% of expressed transcripts showed increased ribosome loading, thereby enhancing translational efficiency. Elevated protein synthesis was accompanied by enhanced phosphorylation of eIF-4E binding protein, suggesting regulation by the mTOR pathway. Some transcripts were under exclusive translational control, including Activated Transcription Factor 5 (ATF5) a b-zip transcription factor, Deleted in Colon Cancer (DCC) the tumor suppressor and Wnt1, the beta-catenin agonist. Parsimonious translation in ESCs may provide a layer of quality control to prevent inappropriate gene expression in the pluripotent state. Experiment Overall Design: Embryonic stem cells (ESC) maintained in an undifferentiated state and day-5 Embryoid bodies (EB) were selected for RNA was extraction and hybridization on Affymetrix 430_2 mouse expression arrays. For polysome fractionation, twelve fractions collected from the gradients were combined to form four pools. One ml of each pool (Pools: 1-4) was used for RNA isolation, labeling and hybridization for undifferentiated ESCs (UD1, UD2, UD3 and UD4) and EBs (EB1, EB2, EB3 and EB4). In parallel, total RNA was also isolated from unfractionated lysates for transcript abundance analysis. Three biological replicates of ESCs and EB cultures were used for polysome fractionation and total RNA analysis.

2008-06-20 | E-GEOD-9563 | biostudies-arrayexpress

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data