Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

P-body mediated translational control in photomorphogenesis

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE107892 | GEO | 2019/06/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

photomorphogenesis-Expression profile of DET1-1 mutant during photomorphogenesis

Project description:rs09-01_det1 - photomorphogenesis - - Identification of the genes deregulated in det1-1 when seedlings grow in light or in dark (dark increase morphological differences between det1-1 and wild-type) - Expression profile of seedlings grown in dark then exposed to light - etiolated seedlings (5days) are briefly exposed to light to induce developmental transition between skoto- and photomorphogenesis without visible change in plant morphology and differences between col0 and the mutant det1-1 grown in light or in dark Keywords: treatment variations

2010-05-01 | GSE19843 | GEO

COP9 signalosome (csn) mutant analysis

Project description:Transcript profiling analysis of csn3-1, csn4-1 and csn5 (csn5a-2 csn5b) light grown and dark grown mutant seedlings compared to light grown and dark grown wild type using Arabidopsis ATH1 GeneChip array Keywords: mutant analysis, growth condition analysis

2008-04-24 | GSE9728 | GEO

Genome-wide identification of PIF4-binding sites and direct-target genes of PIF4 transcriptional regulation in skotomorphogenesis

Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF4, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF4 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis.

2014-10-02 | GSE43284 | GEO

Genome-wide identification of PIF1-binding sites and direct-target genes of PIF1 transcriptional regulation in skotomorphogenesis

Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF1 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis.

2014-10-02 | GSE43283 | GEO

Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [ChIP-Seq]

Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis.

2013-02-01 | GSE39215 | GEO

Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [RNA-Seq]

Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis.

2013-02-01 | GSE39214 | GEO

Interaction between gibberellins and brassinosteroids during etiolated growth in Arabidopsis.

Project description:The proper transition between the skotomorphogenic and photomorphogenic developmental programs is key for seedling survival and it is therefore tightly regulated. Besides light, which is the major cue that triggers this transition, several hormone pathways participate in this control, mainly antagonizing the light effect. Two of these hormones are gibberellins (GA) and brassinosteroids (BR). Both hormones promote the skotomorphogenesis and prevent photomorphogenesis, as evidenced by the partially de-etiolated phenotype caused by GA or BR deficiency, or by a blockage in the respective signaling pathways. We have previously shown that BR mediate GA activity in the control of this transition. For instance, treatment of dark-grown, GA-deficient seedlings with BRs was able to partially restore morphological phenotypes such as hypocotyl growth, and importantly to restore completely the molecular phenotype of CAB2 and RbcS gene expression. On the contrary, GA-treatment did not alter the same phenotypes in the BR deficient det2 mutant. Thus, the aim of this study was to investigate to what extent BRs mediate GA activity in dark-grown seedlings, and for that purpose we have the examined global changes in gene expression caused by treatment with GA and BRs in BR- and GA-deficient seedlings, respectively.

2012-08-02 | GSE32889 | GEO

Photoreceptor control of shoot meristem activity and leaf initiation

Project description:When Arabidopsis seedlings are grown in the dark, their shoot meristem remains in a repressed state and does not develop leaves. The tight control of leaf development by light provides the opportunity to analyse a fundamental plant developmental process in its very early stages. We have observed that activation of photoreceptors in dark-grown seedlings leads to a rapid and dramatic increase in mitotic activity in and around the shoot meristem. Cotyledons also exhibit an induction of cell cycle activity by light, but this consists of endoreduplication and occurs later. Many other processes take place upon induction by light, including the development of the photosynthetic apparatus and the synthesis of sunscreens, but these processes are expected to take place in both the leaf primordia and the cotyledons. We have used this information to carry out a whole transcriptome analysis of shoot meristem activation and early stages of leaf development by light. For this we dissected the shoot apical regions from seedlings grown in the dark or 1, 2, 6, 24, 48 or 72 h after transfer to light. We also dissected cotyledons from equivalent seedlings grown in the dark or 1 or 6 h after transfer to light. From these samples we obtained RNA used for hybridisations against the ATH1 GenChip.

2009-12-05 | GSE19261 | GEO

Increased sucrose levels mediate selective mRNA translation in Arabidopsis

Project description:Background Protein synthesis is a highly energy demanding process and is regulated according to energy availability in plant cells. Light and sugar availability affect mRNA translation but the specific roles of these factors remain unclear. In this study, sucrose was applied to Arabidopsis seedlings kept in the light or in the dark, in order to distinguish sucrose and light effects on transcription and translation. These were studied using microarray analysis of steady state mRNA and mRNA bound to translating ribosomes. Results Steady state mRNA levels were affected differently by sucrose in the light and in the dark but general translation increased to a similar extend in both conditions. Alterations in polysomal mRNA association closely followed the changes induced on the transcript level. However, for 243 mRNAs, a change in ribosome occupancy was observed after sucrose treatment in the light, but not in the dark condition. Many of these mRNAs are annotated as encoding ribosomal proteins, supporting specific translational regulation of this group of transcripts. Unexpectedly, the numbers of ribosomes bound to each mRNA decreased for mRNAs with increased ribosome occupancy. Conclusions Our results suggest that sucrose regulate translation of these 243 mRNAs but specifically in the light, through a novel regulatory mechanism. Our data sows that increased polysomal association is not necessarily leading to more ribosomes per transcript, suggesting a mechanism of translational induction not solely dependent on increased translation initiation rates.

2015-01-28 | GSE59306 | GEO

Dynamic changes of Arabidopsis cis-NAT pairs during de-etiolation

Project description:We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To investigate the role of NATs in response to white light treatment, we designed an Agilent custom array, ATH NAT array, and analyzed WT seedlings grown in the dark (0h) and seedlings undergoing de-etiolation in continuous white light for 1h and 6h. To obtain information on organ-specific transcriptome profiles, we further dissected seedlings into cotyledons, hypocotyls and roots.

2013-12-23 | GSE49382 | GEO

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