Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Translational landscape of photomorphogenic Arabidopsis

ABSTRACT: We report the application of ribosome profiling method to map ribosome locations on transcripts in de-etiolating Arabidopsis seedlings Examine steady-state mRNA and ribosome-protected mRNA abundance in 4-day-old etiolated seedlings with/without 4-h light treatment

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Ming-Jung Liu

PROVIDER: E-GEOD-43703 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Translational landscape of photomorphogenic Arabidopsis.

Liu Ming-Jung MJ Wu Szu-Hsien SH Wu Jing-Fen JF Lin Wen-Dar WD Wu Yi-Chen YC Tsai Tsung-Ying TY Tsai Huang-Lung HL Wu Shu-Hsing SH

The Plant cell 20131031 10

Translational control plays a vital role in regulating gene expression. To decipher the molecular basis of translational regulation in photomorphogenic Arabidopsis thaliana, we adopted a ribosome profiling method to map the genome-wide positions of translating ribosomes in Arabidopsis etiolated seedlings in the dark and after light exposure. We found that, in Arabidopsis, a translating ribosome protects an ~30-nucleotide region and moves in three-nucleotide periodicity, characteristics also obse ...[more]

PMID: 24179124

Similar Datasets

Translational control: a new dimension in the regulation of Arabidopsis photomorphogenesis

Project description:The environmental “light” plays a vital role in regulating the plant growth and development. Transcriptomic profilings were widely used to examine how light regulates the changes of mRNA populations at a genome-wide scale. However, it remains unclear if translational regulation represents a new dimension of gene expression regulation in response to the light signal. Through a transcriptomic comparison of steady-state and polysome-bound mRNAs, we revealed an increased translational efficiency in de-etiolating Arabidopsis seedlings. Over 3,500 genes are subjected to translational regulation whereas only about 770 genes have increased mRNA abundances in response to the light signal. This result suggests a stronger impact of translational control over transcriptomic changes during photomorphogenesis. Genes encoding ribosomal protein are preferentially regulated at the translational level, possibly contributing to the enhancement of translation efficiency as observed. We also uncovered mRNAs regulated at the translational level share characteristics of longer half-lives and shorter cDNA length. The presence of a cis-element, TAGGGTTT, in the 5’untranslated region of a transcript renders its translational regulation by light signals. Taken together, our study revealed a previously neglected aspect of gene expression regulation during Arabidopsis photomorphogenesis. The identities and molecular signatures associated with mRNAs regulated at the translational level also offer new directions to perform mechanistic studies of light-trigged translational enhancement in Arabidopsis. Three biological replicates for 4-d-old etiolated seedlings with or without 0. 5 h or 4 h of white-light treatment.

2012-07-10 | E-GEOD-29657 | biostudies-arrayexpress

Expression data from Arabidopsis thaliana seedlings with reduced synthesis of 5-aminolevulinic acid

Project description:5-aminolevulinic acid (ALA) is the common precursor of all biological synthezised tetrapyrroles. Inhibition of ALA synthesis results in decreased amounts of chlorophylls, heme, siroheme and phytochrome. It was previously shown that 4 out of 5 Arabidopsis mutants uncoupling nuclear gene expression from the physiological state of the chloroplast are affected in plant tetrapyrrole biosynthesis. It is common to all four mutants to show a reduced ALA formation. We investigate the impact of reduced plastidic ALA synthesis on nuclear gene expression by inhibition of ALA formation using gabaculin and compare these effects with the gun4-1 mutant. Formation of 5-aminolevulinic acid was inhibited in Arabidopsis thaliana Col-0 seedlings by application of 10 µM gabaculin. Additionally the Arabidopsis gun4-1 mutant was investigated. Seedlings were etiolated for 3 days on MS medium in absence or presence of gabaculin and subsequently deetiolated for 6 hours. Total RNA was extracted and used for microarray hybridisation.

2011-04-01 | E-GEOD-27704 | biostudies-arrayexpress

Evolution of Translation Regulation in budding Yeast

Project description:Comparison of translation efficiency in S. cerevisiae, S. paradoxus, and their F1 hybrid. SRA submission number SRP028552; BioProject number PRJNA213844; Ribosome profiling was used to compare mRNA abundance, ribosome occupancy, and translation efficiency in two yeast species and their F1 hybrid.

2013-12-04 | E-GEOD-52119 | biostudies-arrayexpress

Transcription profiling of Arabidopsis etiolated seedlings, light-treated seedlings, leaves and flowers hybridized to ATH1 and AGRONOMICS1 arrays

Project description:RNA from etiolated seedlings, light-treated seedlings, leaves and flowers was hybridized to ATH1 and AGRONOMICS1 arrays.

2010-01-01 | E-MEXP-2472 | biostudies-arrayexpress

Translational landscape of photomorphogenic Arabidopsis

Project description:We report the application of ribosome profiling method to map ribosome locations on transcripts in de-etiolating Arabidopsis seedlings

2013-11-08 | GSE43703 | GEO

Ribosome Profiling over a Zebrafish Developmental Timecourse

Project description:To experimentally-validate the non-coding status of annotated lncRNAs, we performed ribosome profiling over a developmental timecourse that matched our previously-published (Pauli et al. 2012) developmental transcriptome. We find that many previously-annotated lncRNAs appear to be translated, but in a pattern more akin to 5' leaders of coding genes. Ribosome profiling over 8 stages in early zebrafish development: 2-4 cell, 256 cell, 1K cell, Dome, Shield, Bud, 28hpf and 5dpf

2013-05-23 | E-GEOD-46512 | biostudies-arrayexpress

P-body mediated translational control in photomorphogenesis

Project description:Light, an important environmental factor regulates most of plant physiology and development. In the photomorphogenic stage, light globally enhances translation status in de-etiolating Arabidopsis seedlings. More than 1500 genes showed increased translation but not transcription in this developmental process. This implies these mRNAs are translationally repressed in dark-grown seedlings. Through transcriptome and translatome comparisons, we revealed that p-bodies attenuate the translation of mRNAs in the etiolated seedlings. We found hundreds of mRNAs accumulated and also increased translation for thousands of genes in dark-grown dcp5-1, including genes known to regulate the transition from skotomorphogenesis to photomorphogenesis. Our data reports p-bodies regulate both RNA stability and attenuation of translation for specific mRNAs in the dark.

2019-06-20 | GSE107892 | GEO

Transcriptomics analysis of etiolated Arabidopsis thaliana seedlings in response to microgravity

Project description:Gene expression profile of two-week-old etiolated Arabidopsis seedlings under microgravity on board space flight BRIC16 were compared with ground grown control in both wild-type and act2-3 mutant plants.

2015-09-15 | E-MTAB-3011 | biostudies-arrayexpress

Mapping the castor bean endosperm proteome revealed a metabolic interaction between plastid, mitochondria, and peroxisomes to optimize seedling growth

Project description:The aim of the project was to elucidate the inter-organellar interplay of plastids, mitochondria, and peroxisomes during storage reserve mobilization in the endosperm to supply the growing seedling with nutrients upon germination. Organelles from endosperm of etiolated castor bean seedlings were isolated and subjected to liquid chromatography-tandem mass spectrometry. The data were used to build a comprehensive metabolic model for plastids, mitochondria, and peroxisomes.

2024-01-09 | PXD040932 | Pride

Nitric Oxide Enhances Resistance to PEG-induced Water Deficiency is Associated with the Primary Photosynthesis Reaction in Triticum aestivum L.

Project description:Photosynthesis is affected by water deficiency (WD) stress, and nitric oxide (NO) is a free radical that participates in the photosynthesis process. Previous studies have suggested that NO regulates the excitation energy distribution of photosynthesis under WD stress. Here, quantitative phosphoproteomic profiling was conducted using isobaric tags for relative and absolute quantitation. Differentially phosphorylated protein species (DEPs) were identified in leaves of NO or polyethylene glycol (PEG)-treated wheat seedlings (D) and in control seedlings, 2,257 unique phosphorylated peptides and 2,416 phosphorylation sites were identified from 1,396 unique phosphoproteins. Of these, 96 DEPs displayed significant changes (≥ 1.50-fold, p < 0.01). These DEPs are involved in photosynthesis and signal transduction, etc. Furthermore, phosphorylation of several DEPs were up-regulated by both D and NO treatments, but down-regulated only in NO treatment. These differences affected the chlorophyll A-B binding protein, chloroplast post-illumination chlorophyll fluorescence increase protein, and SNT7, implying that NO indirectly regulated the absorption and transport of light energy in photosynthesis in response to WD stress. The significant difference of chlorophyll (Chl) content, Chl a fluorescence transient, photosynthesis index, and trapping and transport of light energy further indicated that exogenous NO under D stress enhanced the primary reaction of photosynthesis compared to D treatment. A putative pathway is proposed to elucidate NO regulation of the primary reaction of photosynthesis under WD.

2019-11-14 | PXD010724 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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