Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA320878 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3480150.fastq.gz | Fastqsanger.gz | |||
| SRR3480160.fastq.gz | Fastqsanger.gz | |||
| SRR3480170.fastq.gz | Fastqsanger.gz | |||
| SRR3480180.fastq.gz | Fastqsanger.gz | |||
| SRR3480190.fastq.gz | Fastqsanger.gz |
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Project description:In response to neighbor proximity plants increase growth of specific organs (e.g. hypocotyl) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing those bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we analyzed changes in transcript abundance at different time points during a shade treatment in dissected cotyledons and hypocotyls. We concentrated our analysis on these two organs because the former is considered as the primary shade-sensing organ while elongation is rapidly triggered in the hypocotyl. We conclude that PIFs initiate transcriptional reprogramming in both organs within 15 minutes comprising regulated expression of several early auxin response genes. This suggests that hypocotyl growth is elicited by both local and distal auxin signals. With time the transcriptional response diverges increasingly between organs. We identify genes whose differential expression may underlie organ-specific elongation. Finally, we uncover a growth promotion gene expression signature shared between responses to different environments and organs.
2017-01-17 | GSE81202 | GEO
Project description:This study aims to identify genes which help to understand similar underlying mechanism in the response to shade and wounding in Arabidopsis thaliana plants.
2022-05-12 | GSE133252 | GEO
Project description:Growth of a complex multicellular organism requires coordinated changes in diverse cell types. These cellular changes generate organs of the correct size, shape and functionality. During plant development, the growth hormone auxin induces stem elongation; however, which cell types of the stem perceive the auxin signal and contribute to organ growth is poorly understood. Here, we show that auxin signalling is required in many cell types for correct hypocotyl stem growth, with a key role for the epidermis. Combining genetic manipulations in Arabidopsis thaliana with transcriptional profiling of the hypocotyl epidermis from Brassica rapa, we show that auxin functions in the epidermis in part by inducing activity of the locally-acting, growth-promoting brassinosteroid pathway. Our findings clarify cell-specific auxin function in the hypocotyl, and highlight the complexity of cell-type interactions within a growing organ. We performed whole-genome transcriptome (mRNA-Seq) on 5 d-old W light-grown Arabidopsis thaliana plants (CER6pro>>axr3-1::mCit experimental plants and UAS::axr3-1::mCit hemizygous control plants; whole-seedling tissue) treated for 4 h W light or low R:FR shade. In addition, we performed mRNA-Seq on 4 d-old Brassica rapa plants (FPsc strain) treated for 9 h W light or shade. Brassica tissues collected were hypocotyl epidermal peels or whole hypocotyls.
2016-06-30 | E-GEOD-79881 | biostudies-arrayexpress
Project description:The growth of plant organs is driven by cell division and subsequent cell expansion. The transition from proliferation into expansion is critical for the final organ size and, consequently plant yield. Exit from proliferation and onset of expansion is accompanied by major metabolic reprogramming, and in leaves with the establishment of photosynthesis. To learn more about the molecular mechanisms underlying the developmental and metabolic transitions important for plant growth, we used untargeted proteomics and metabolomics analyses to profile young leaves of a model plant Arabidopsis thaliana representing proliferation, transition, and expansion stages. The third true leaves of the in vitro grown Arabidopsis seedlings were harvested daily from day 8 to day 13 after stratification (8 to 13 DAS). Days 8 and 9 correspond to proliferation, days 12 and 13 to expansion and days 10 and 11 to the transition. The dataset presented represents a unique resource comprising approximately 4000 proteins and 300 annotated small-molecular compounds measured across six consecutive days of leaf growth. These can now be mined for novel developmental and metabolic regulators of plant growth and can act as a blueprint for future studies aimed at better defining the interface of development and metabolism in any other species.
2021-09-09 | PXD019545 | Pride
Project description:Plants have evolved shoot elongation mechanisms to escape from diverse environmental stresses such as flooding and vegetative shade. The apparent similarity in growth responses suggests possible convergence of the signalling pathways. Shoot elongation is mediated by passive ethylene accumulating in flooded plant organs and by changes in light quality and quantity under vegetation shade. Here we study hypocotyl elongation as a proxy for shoot elongation and delineated Arabidopsis hypocotyl length kinetics in response to ethylene and shade. Based on these kinetics, we further investigated ethylene and shade-induced genome-wide gene expression changes in hypocotyls and cotyledons separately. Both treatments induced a more extensive transcriptome reconfiguration in the hypocotyls compared to the cotyledons. Bioinformatics analyses suggested contrasting regulation of growth promotion- and photosynthesis-related genes. These analyses also suggested an induction of auxin, brassinosteroid and gibberellin signatures and the involvement of several candidate regulators in the elongating hypocotyls. Pharmacological and mutant analyses confirmed the functional involvement of several of these candidate genes and physiological control points in regulating stress-escape responses to different environmental stimuli. We discuss how these signaling networks might be integrated and conclude that plants, when facing different stresses, utilise a conserved set of transcriptionally regulated genes to modulate and fine tune growth. 1 day old Arabidopsis seedlings were subjected to control, ethylene and shade conditions. Hypocotyl and cotyledon tissues were harvested at 1.5 h, 13.5 h and 25.5 h of treatment time respectively. Microarray hybridization was carried out with 3 biological replicates (collected over 3 independent experiments) of each sample using the Affymetrix Arabidopsis Gene 1.1 ST platform.
2016-06-10 | E-GEOD-83212 | biostudies-arrayexpress
Project description:To investigate the effect of simulated shade on the genetic network regulating ovule development, we treated Arabidopsis adult plants with W or simulated shade (W+FR) for up to 24 h. After extracting total RNA from floral buds we performed gene expression profiling analysis using data from RNA-seq of two different treatments at different time points
2025-01-15 | GSE230448 | GEO
Project description:Spatiotemporal brassinosteroid signaling and antagonism with auxin control Arabidopsis root growth.
| PRJNA230565 | ENA
Project description:Shade can trigger the shade avoidance syndrome (SAS) in shade-intolerant species,which cause exaggerated growth and affect crop yield.We report that Arabidopsis transcription factors bZIP59 negatively regulate SAS. To investigate the function of bZIP59 during SAS, we performed RNA-Seq of wild type Col-0 and a T-DNA insertion line bzip59 (SALK_024459) in while light and shade.
2024-08-18 | GSE227154 | GEO
Project description:Shade avoidance syndrome (SAS) is a strategy of major adaptive significance that includes the elongation of vegetative structures and leaf hyponasty. Major transcriptional rearrangements underlie for the reallocation of resources to elongate vegetative structures and redefine the plant architecture under shade to compete for photosynthesis light. BBX28 is a transcription factor involved in seedling de-etiolation and flowering in Arabidopsis thaliana, but its function in the SAS is completely unknown. Here we studied the function of BBX28 in the regulation of gene expression under simulated shade conditions.
2024-03-15 | GSE217723 | GEO