Project description:miRNA profile of wild type Arabidopsis plants was compared to miRNA profiles in three different lines with altered levels of ascorbate (vtc2-1), glutathione (pad2-1) or salicylate (nahG).
Project description:To uncover the possible regulatory mechanism in regulatory alternative splicing in plants evolution, we used RNA-seq to compare the transcriptomes in Arabidopsis ecotypes Col and C24. We found different class of AS types have different regulatory mechanisms in Arabidopsis and divergence of alternative splicing in different class is varied in evolution. Sequence variation analysis had found evolution divergent AS events significantly altered their sequences compared to conserved events and the variation is AS class specific.
Project description:LKP2 belongs to a group of blue light receptors in Arabidopsis thaliana. We performed DNA microarray analysis to identify genes whose expression levels are altered in LKP2-overexpressing plants. Agilent's Whole Arabidopsis Genome Oligo Microarray (G2519F, V4, 4x44K) was used.
Project description:Alternative splicing (AS) generates transcript variants by the definition of different exonic and intronic regions and causes a massive expansion of transcriptome diversity. Changes in AS patterns have been found to be linked to manifold biological processes, yet fundamental aspects such as the regulation of AS and the functional implications of altered AS programs largely remain to be addressed. In this work, widespread AS regulation by Arabidopsis Polypyrimidine tract-binding protein homologues (AtPTBs) was revealed. In total 452 AS events derived from 308 distinct genes were found to be responsive to the levels of the splicing factors AtPTB1 and AtPTB2, which predominantly triggered splicing of regulated introns, inclusion of cassette exons, and usage of upstream 5' splice sites. In contrast, alternative 3' splice site events were strongly underrepresented among the AtPTB1/2 targets and no major AS regulatory function of the distantly related AtPTB3 was found. Dependent on their position within the mRNA, AtPTB-regulated events can both modify the untranslated regions and give rise to alternative protein products. Gene ontology analysis revealed a connection of AtPTB-mediated AS control with diverse biological processes, and the functional implications of selected AS events were further elucidated in the context of seed germination and flowering time control. Specifically, AtPTB misexpression changes AS of the PHYTOCHROME INTERACTING FACTOR 6 (PIF6) pre-mRNA, coinciding with altered rates of abscisic acid-dependent seed germination. Furthermore, AS patterns as well as the expression of key flowering regulators were massively changed in an AtPTB1/2 level-dependent manner. In conclusion, our work has revealed widespread AS regulatory functions of the AtPTB splicing factors with important functional implications in various fundamental processes of Arabidopsis development. Analysis of alternative splicing patterns in plants with increased and decreased levels of the 3 Arabidopsis Polypyrimidine-tract binding protein homologues in comparison to wild type samples, determined in duplicates
Project description:LKP2 belongs to a group of blue light receptors in Arabidopsis thaliana. We performed DNA microarray analysis to identify genes whose expression levels are altered in LKP2-overexpressing plants. Agilent's Whole Arabidopsis Genome Oligo Microarray (G2519F, V4, 4x44K) was used. Comparison between 35S:GFP overexpressing- and 35S:GFP-LKP2 overexpressing- plants (Yasuhara et al. 2004) was performed.
Project description:Plants developed a plasticity to eviromental conditions, such as temperaure, that allows their adaptation. A change in ambient temperature leads to changes in the transcriptome in plants, such as the production of different splicing isoforms. Here we study temperature induced alternative splicing events in Arabidopsis thaliana wild-type and two epigentic mutants, sdg8-2 and sdg26-1 using an RNA-seq approach.
Project description:Comparison of plants that overexpress PK12 and non-transformed plants. Plants were grown for 10 days under long day conditions (GSM3816-GSM3819) or plants were grown for 21 days under long day conditions (GSM3820-GSM3823) . Hybridization was performed on arrays from Arabidopsis Keck Resource Lab Array (Yale University) containing 12K (GSM3816-GSM3819) or 9K (GSM3820-GSM3823)Arabidopsis ESTs. The 4 samples corresponding to each array represent 2 repetitions of 2 independent biological experiments. Keywords = Alternative splicing Keywords = phosphorylation Keywords: equivalent probe
2003-02-05 | GSE274 | GEO
Project description:Root microbiome of Arabidopsis plants with altered phosphate starvation response
Project description:Analysis of transcriptional profiling of Arabidopsis Col-0 leaves from wild-type and plants with incresed levels of AtOXR2 (oeOXR2 plants)