Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA98157 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome-wide expression analysis regulated by internal nitrate in the presence of external ammonium in Arabidopsis thaliana
| PRJDB8627 | ENA
Project description:Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls the plant response to day length, is one of the most important pathways controlling flowering. In Arabidopsis photoperiodic flowering, CONSTANS (CO) is the central gene activating the expression of the florigen FLOWERING LOCUS T (FT) in the leaves at the end of a long day. CO expression is strongly regulated by the circadian clock. However, to date, no evidence has been reported regarding a feedback loop from the photoperiod pathway back to the circadian clock. Using transcriptional networks, we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway. Gene expression, chromatin immunoprecipitation experiments and phenotypic analysis allowed us to elucidate the role of CO over the circadian clock. Plants with altered CO expression showed a different internal clock period, measured by daily rhythmic movements in the leaves. We show that CO is able to activate key genes related to the circadian clock, such as CCA1, LHY, PRR5 and GI, at the end of a long day by binding to specific sites on their promoters. Moreover, a significant number of PRR5 repressed target genes are upregulated by CO, and this could explain the phase transition promoted by CO. The CO-PRR5 complex interacts with the bZIP transcription factor HY5 and helps to localize the complex in the promoters of clock genes. Our results indicate that there may be a feedback loop in which CO communicates back to the circadian clock, feeding seasonal information to the circadian system.
2023-08-01 | GSE236178 | GEO
Project description:Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls the plant response to day length, is one of the most important pathways controlling flowering. In Arabidopsis photoperiodic flowering, CONSTANS (CO) is the central gene activating the expression of the florigen FLOWERING LOCUS T (FT) in the leaves at the end of a long day. CO expression is strongly regulated by the circadian clock. However, to date, no evidence has been reported regarding a feedback loop from the photoperiod pathway back to the circadian clock. Using transcriptional networks, we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway. Gene expression, chromatin immunoprecipitation experiments and phenotypic analysis allowed us to elucidate the role of CO over the circadian clock. Plants with altered CO expression showed a different internal clock period, measured by daily rhythmic movements in the leaves. We show that CO is able to activate key genes related to the circadian clock, such as CCA1, LHY, PRR5 and GI, at the end of a long day by binding to specific sites on their promoters. Moreover, a significant number of PRR5 repressed target genes are upregulated by CO, and this could explain the phase transition promoted by CO. The CO-PRR5 complex interacts with the bZIP transcription factor HY5 and helps to localize the complex in the promoters of clock genes. Our results indicate that there may be a feedback loop in which CO communicates back to the circadian clock, feeding seasonal information to the circadian system.
2024-01-01 | GSE222657 | GEO
Project description:Plants respond to seasonal cues such as the photoperiod, to adapt to current conditions and to prepare for environmental changes in the season to come. To assess photoperiodic responses at the protein level, we quantified the proteome of the model plant Arabidopsis thaliana by mass spectrometry across four photoperiods. This revealed coordinated changes of abundance in the proteins of photosynthesis, primary metabolism and secondary metabolic processes such as pigment biosynthesis, consistent with higher metabolic activity in long photoperiods. Higher translation rates during the day than during the night likely contribute to these changes, but rhythmic RNA profiles will alter their effects. Photoperiodic control of protein levels might be greatest if high translation rates only coincide with high transcript levels in some photoperiods. We term this mechanism ‘translational coincidence’, mathematically model its components, and demonstrate its effect on the Arabidopsis proteome. Datasets from a green alga and a cyanobacterium suggest that this mechanism is general, contributing to the seasonal control of the proteome in many phototrophic organisms, and favouring RNA rhythms even for stable proteins.
2018-02-27 | PXD006848 | Pride
Project description:The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation. The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light. In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation. Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5.
2011-03-31 | GSE21684 | GEO
Project description:Most higher organisms, including plants and animals, have developed a time-keeping mechanism that allows them to anticipate daily fluctuations of environmental parameters such as light and temperature. This circadian clock efficiently coordinates plant growth and metabolism with respect to time-of-day by producing self-sustained rhythms of gene expression with an approximately 24-hour period. The importance of these rhythms has in fact been demonstrated in both phytoplankton and higher plants: organisms that have an internal clock period matched to the external environment possess a competitive advantage over those that do not. We used microarrays to identify circadian-regulated genes of Arabidopsis thaliana to elucidate how the clock provides an adaptive advantage by understanding how the clock regulates outputs and determining which pathways and processes may be under circadian control. Keywords: time course
2007-07-15 | GSE8365 | GEO
Project description:Interaction between gibberellins and brassinosteroids during etiolated growth in Arabidopsis.
| PRJNA146625 | ENA
Project description:We performed a time course analysis (TC data set) of the response of whole seedling roots to 140mM NaCl at 5 time points after transfer (30 minutes, 1, 4, 16 and 32 hours). Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states. While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli. Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis. Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment. We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers. To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types. Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression. Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered. Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context. Experiment Overall Design: Seedlings were grown for 4-5 days before transfer to standard media supplemented with 140 mM NaCl. Whole roots were harvested at 5 time points after the transfer.
2009-04-25 | E-GEOD-7642 | biostudies-arrayexpress
Project description:As multicellular organisms, plants must integrate responses to environmental cues across different cell types and also over time. Nitrate is the major source of available Nitrogen for plants, and a limiting factor for plant growth and productivity. Plant root s are highly impacted by nitrate availability, modifying their architecture to optimize nitrate uptake from soils. In order to understand how this functional response is dynamically orchestrated across different cell types of the root, space and time must be addressed within the same experimental setup. We performed a transcriptomic analysis in five major root cell types of Arabidopsis plants in response to nitrate treatments considering short and long time exposure to this macronutrient. We found nitrate treatment triggers a dynamic reprogramming of root cell gene expression that follows a spatial pattern over time consistent with an early regulation of nitrate transport and assimilation in external layers of the root and a later regulation of hormonal and developmental processes in more internal layers of the root.
2022-01-01 | E-MTAB-9519 | biostudies-arrayexpress
Project description:The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
| PRJNA97693 | ENA