Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcript levels in Arabidopsis thaliana over a 24-hour diurnal cycle

ABSTRACT: Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830).

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE61895 | GEO | 2015/10/15

SECONDARY ACCESSION(S): PRJNA262637

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Polysome profiling in Arabidopsis thaliana over a 24-hour diurnal cycle

2015-10-15 | GSE61897 | GEO

Transcript levels in Arabidopsis thaliana over a 24-hour diurnal cycle

Project description:Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830). 10 day-old wild type and CCA1-ox (described in Cell. 1998 Jun 26;93(7):1207-17) Arabidopsis seedlings were harvested at 6am (Zeitgeber time ZT0), 12pm (ZT6), 6pm (ZT12), and 12am (ZT18), with 3 replicates for each time and genotype.

2015-02-01 | E-GEOD-61895 | biostudies-arrayexpress

Polysome profiling in Arabidopsis thaliana over a 24-hour diurnal cycle

2015-02-01 | E-GEOD-61897 | biostudies-arrayexpress

Polysome profiling in CIRCADIAN CLOCK ASSOCIATED 1-overexpressing (CCA1-ox) Arabidopsis thaliana over a 24-hour diurnal cycle

2015-10-15 | GSE61898 | GEO

Transcript levels in CIRCADIAN CLOCK ASSOCIATED 1-overexpressing (CCA1-ox) Arabidopsis thaliana over a 24-hour diurnal cycle

2015-10-15 | GSE61896 | GEO

Transcript levels in CIRCADIAN CLOCK ASSOCIATED 1-overexpressing (CCA1-ox) Arabidopsis thaliana over a 24-hour diurnal cycle

2015-02-01 | E-GEOD-61896 | biostudies-arrayexpress

Polysome profiling in CIRCADIAN CLOCK ASSOCIATED 1-overexpressing (CCA1-ox) Arabidopsis thaliana over a 24-hour diurnal cycle

2015-02-01 | E-GEOD-61898 | biostudies-arrayexpress

Diurnal and Circadian-Regulated Genes in Arabidopsis

Project description:Plants respond to day/night cycling in a number of physiological ways. At the mRNA level, the expression of some genes changes during the 24-hr period. To identify novel genes regulated in this way, we used microarrays containing 11,521 Arabidopsis expressed sequence tags, representing an estimated 7800 unique genes, to determine gene expression levels at 6-hr intervals throughout the day. Eleven percent of the genes, encompassing genes expressed at both high and low levels, showed a diurnal expression pattern. Approximately 2% cycled with a circadian rhythm. By clustering microarray data from 47 additional, unrelated experiments, we identified groups of genes regulated only by the circadian clock. These groups contained the already characterized clock-associated genes LHY, CCA1, and GI, suggesting that other key circadian clock genes might be found within these clusters. This research has been described more fully in Schaffer R et al.(2001) Plant Cell 13:113-123 Keywords = circadian rhythm Keywords: other

2001-07-20 | GSE4 | GEO

Genome-wide Identification of CCA1 Targets Uncovers an Expanded Clock Network in Arabidopsis

Project description:The plant circadian clock exerts a critical role in the regulation of multiple biological processes including responses to biotic and abiotic stresses. It is estimated that the clock regulates up to 80% of the transcriptome in Arabidopsis, thus understanding the molecular mechanisms that control this rhythmic transcriptome requires identification of the targets of each clock component. The Arabidopsis core clock is partially comprised of a transcriptional regulatory loop between the MYB domain containing transcription factors CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and TIMING OF CAB EXPRESSION1 (TOC1). As a key component of the clock, CCA1 is able to initiate and set the phase of clock-controlled rhythms. CCA1 regulates the transcription of several genes by directly binding to the evening element (EE) motif primarily found in the promoters of evening expressed genes. Using a genome-wide approach we have identified direct targets of CCA1 in plants grown in constant (LL) and driven conditions (LD). These CCA1 targets are enriched for a myriad of biological processes and stress responses. While many of these target genes are evening phased and contain the EE in their promoter regions, a significant subset is morning phased and lack an EE. Furthermore, several CCA1 targets do not cycle in either LL or LD or both. Expression analysis in CCA1 overexpressing plants confirms CCA1 regulation of analyzed targets. Our results emphasize an expanded role for the circadian clock in regulation of key pathways in Arabidopsis, and provide a comprehensive and solid resource for future functional studies. ChIP-Seq of CCA1-GFP plants under control of the CCA1 promoter in continuous light and diel conditions

2015-07-26 | E-GEOD-70533 | biostudies-arrayexpress

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [ChIP-Seq]

Project description:Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. Core circadian clock genes related chromatin connectivity networks suggested they co-localized within the same ?transcriptional factory? and define a distinct nuclear landscape and circadian outputs in the AM and PM. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal a distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.

2021-12-24 | GSE143719 | 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