Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA283114 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Cold stress, which adversely affects plants growth and development, regulates the transcription and splicing of plants splicing factors. This affects the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions. Two-week old Arabidopsis seedlings grown on agar were subjected to 24 hours of cold (4°C) treatment under long day conditions. Control and cold-treated plants were harvested at the same time to ensure that observed differences would not be due to circadian clock effects on transcripts. Total RNA from four biological repeats were used for microarray hybridization.
2013-05-12 | E-GEOD-35996 | biostudies-arrayexpress
Project description:Purpose: Circadian clock in plants temporally coordinates biological processes throughout the day synchronizing gene expression with environmental changes. Here, we examined the genome-wide circadian and diurnal control of Arabidopsis transcriptome using high throughout RNA-seq approach. Methods: Transcriptional and posttranscritional profiles were identified and characterized for Arabidopsis seedlings grown under continuous light or long-day condition (16 h light/8 h dark) for one day (each condition has two biological replicates). Results: We show that rhythmic posttranscriptional regulation is also a significant factor for genome-wide profile of circadian plant transcriptome. Two major posttranscriptioal mechanisms alternative splicing (AS) and alternative polyadenylation (APA) show circadian rhythmicity, resulting from the oscillation in the genes invovled in AS and APA. Conclusions: Arabidopsis circadian clock not only controls the transcription of genes, but also affects their posttranscriptional regulation through regulating AS and APA.
2020-01-14 | GSE137732 | GEO
Project description:UV-B Responses in Light Grown Plants: Similarities to Biotic Stress
| PRJNA97037 | ENA
Project description:Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Cold stress, which adversely affects plants growth and development, regulates the transcription and splicing of plants splicing factors. This affects the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions.
2013-05-12 | GSE35996 | GEO
Project description:Plants were germinated in white light and then either grown in WL (white light) or far-red enriched white light (WL+FR)
2020-02-03 | GSE137009 | GEO
Project description:The goal of this project is to compare the primary metabolite profile in different tissue types of the model plant Arabidopsis thaliana. Specifically, plants were grown hydroponically under the long-day (16hr light/day) condition at 21C. Tissue samples, including leaves, inflorescences, and roots were harvest 4 1/2 weeks post sowing. Untargeted primary metabolites profiling was carried out using GCTOF.
2021-12-09 | ST002012 | MetabolomicsWorkbench
Project description:How do the transcript levels of leaf-expressed genes change in a normal day-night cycle? The interest is in genes that are regulated by the circadian clock and the diurnal component (i.e. light, metabolite changes). Plants were grown on soil in a 12/12 h light/dark rythm at 20°C day and night. 5 weeks after germination the rosettes of the non-flowering plants were harvested, 15 plants per sample. Plants were harvested at 6 timepoints every 4 hours beginning with the end of the night (still in darkness). Keywords: repeat
2005-12-01 | GSE3416 | GEO
Project description:We identified PRP4 kinase-A (PRP4ka) in a forward genetic screen based on an alternatively-spliced GFP reporter gene in Arabidopsis thaliana (Arabidopsis). Prp4 kinase, which was the first spliceosome-associated kinase shown to regulate splicing in fungi and mammals, has not yet been studied in plants. Analysis of RNA-seq data from the prp4ka mutant revealed widespread perturbations in alternative splicing. A quantitative iTRAQ-based phosphoproteomics investigation of the mutant identified phosphorylation changes in several serine/arginine-rich proteins, which regulate constitutive and alternative splicing, as well as other splicing-related factors. The results demonstrate the importance of PRP4ka in alternative splicing and suggest that PRP4ka may influence alternative splicing patterns by phosphorylating a subset of splicing regulators.
2018-10-25 | PXD008580 | Pride
Project description:Light is a pivotal signal for plants’ growth and survival. The promptly responses are required and achieving by sophisticated transcriptomic adjustments, the promptly translation enhancement, and effective protein surveillance. However, the global role of alternative splicing regulations in response to the light is unknown. Through global surveys of alternative splicing profile and frequency calculation for individual events normalized to transcriptomic changes, we identify nearly half of transcript present at this stage are alternatively spliced. Through the unbiased event comparison in D and L4h mRNA, we reveal a clear impact of splicing control on 2,961 genes during early photomorphogenesis. Intron retention is the most frequently event under controls of light as discovered in other developmental tissues and stages of Arabidopsis. Cryptic exon is the most abundant event preserved only in the dark-grown Arabidopsis. Genes underlying the splicing and transcriptional control mostly not overlapped indicate the distinct impacts of two regulatory mechanisms. Through confirmation with a homemade microarray for their responsiveness of light, we conclude 1,792 genes as biological validated candidates. Through functional study for genes underlying light-mediated splicing controls, we explore new light-signaling components which mainly responsive in isoform abundance but steady state mRNA. Among examination both positive (RPR39, KH-RBP, RRM and RRC1) and negative (PIF4, AMI1, DNAJ, UKL3, TF-IIs-like, and ubknown-Golgi protein) factors are controlled by splicing. Through predictions for example isoform structures, PIF4-IR4, AMI1-IR7-IR8, and DNAJ-IR1 both possess PTC and possibly produce truncated coding protein. PIF4-IR4 becomes best illustration for the dysfunction for the negative regulator by light. Above PTC+ isoforms together with one third of retained introns translate that evident for NMD-insensitive retained introns and supplements for protein levels. The event identities and cis-motif signatures associated with light regulations confirm a given uniqueness for the gene expression regulation during Arabidopsis photomorphogenesis. mRNA and polysome-associated mRNA of 4 days old Arabidopsis seedling grown under the dark or with 4 h light-treatment were isolated and the transcriptome and splicing events profiles were surveyed by mRNAseq. Independent 3 biological replicates of dark and L4h mRNA were applied for two-color-microarray using custom designed alternative-splicing array from Agilent Technologies.
2015-07-26 | E-GEOD-49408 | biostudies-arrayexpress
Project description:Light is a pivotal signal for plants’ growth and survival. The promptly responses are required and achieving by sophisticated transcriptomic adjustments, the promptly translation enhancement, and effective protein surveillance. However, the global role of alternative splicing regulations in response to the light is unknown. Through global surveys of alternative splicing profile and frequency calculation for individual events normalized to transcriptomic changes, we identify nearly half of transcript present at this stage are alternatively spliced. Through the unbiased event comparison in D and L4h mRNA, we reveal a clear impact of splicing control on 2,961 genes during early photomorphogenesis. Intron retention is the most frequently event under controls of light as discovered in other developmental tissues and stages of Arabidopsis. Cryptic exon is the most abundant event preserved only in the dark-grown Arabidopsis. Genes underlying the splicing and transcriptional control mostly not overlapped indicate the distinct impacts of two regulatory mechanisms. Through confirmation with a homemade microarray for their responsiveness of light, we conclude 1,792 genes as biological validated candidates. Through functional study for genes underlying light-mediated splicing controls, we explore new light-signaling components which mainly responsive in isoform abundance but steady state mRNA. Among examination both positive (RPR39, KH-RBP, RRM and RRC1) and negative (PIF4, AMI1, DNAJ, UKL3, TF-IIs-like, and ubknown-Golgi protein) factors are controlled by splicing. Through predictions for example isoform structures, PIF4-IR4, AMI1-IR7-IR8, and DNAJ-IR1 both possess PTC and possibly produce truncated coding protein. PIF4-IR4 becomes best illustration for the dysfunction for the negative regulator by light. Above PTC+ isoforms together with one third of retained introns translate that evident for NMD-insensitive retained introns and supplements for protein levels. The event identities and cis-motif signatures associated with light regulations confirm a given uniqueness for the gene expression regulation during Arabidopsis photomorphogenesis. mRNA and polysome-associated mRNA of 4 days old Arabidopsis seedling grown under the dark or with 4 h light-treatment were isolated and the transcriptome and splicing events profiles were surveyed by mRNAseq. Independent 3 biological replicates of dark and L4h mRNA were applied for two-color-microarray using custom designed alternative-splicing array from Agilent Technologies.
2015-07-26 | E-GEOD-49407 | biostudies-arrayexpress