Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA208886 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing, producing two splice variants, FLM-β and FLM-δ, which compete for interaction with the floral repressor SVP. The SVP/FLM-β complex is predominately formed at low temperatures and prevents precocious flowering. In contrast, the competing SVP FLM-δ complex is impaired in DNA binding and acts as a dominant negative activator of flowering at higher temperatures. Our results demonstrate the importance of temperature-dependent alternative splicing in modulating the timing of the floral transition in response to environmental change.
2013-09-19 | GSE48082 | GEO
Project description:How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing, producing two splice variants, FLM-M-NM-2 and FLM-M-NM-4, which compete for interaction with the floral repressor SVP. The SVP/FLM-M-NM-2 complex is predominately formed at low temperatures and prevents precocious flowering. In contrast, the competing SVP FLM-M-NM-4 complex is impaired in DNA binding and acts as a dominant negative activator of flowering at higher temperatures. Our results demonstrate the importance of temperature-dependent alternative splicing in modulating the timing of the floral transition in response to environmental change. ChIP-seq A. thaliana FLM (3 replicates for gFLM and 2 replicates for FLM splice variants)
2013-09-19 | E-GEOD-48082 | biostudies-arrayexpress
Project description:Ambient temperature dependent flowering time is an important feature that is required for plants to reproduce in various environmental conditions. The rising global temperature poses a significant challenge to the growth and reproduction of plants. In Arabidopsis thaliana, FLM-β, a major splicing isoform of the flowering repressor gene FLOWERING LOCUS M, is down-regulated in response to increasing temperature and represents a critical mechanism for plants to respond to temperature changes. However, it is unknown how the transcript level of FLM-β is down-regulated. Here we identify an RRM domain-containing protein, UBA2C, as a previously uncharacterized flowering repressor by forward genetic screening. We demonstrate that UBA2C directly binds to FLM chromatin and facilitates FLM transcription predominantly by inhibiting the histone H3K27 trimethylation, a histone mark related to transcriptional repression. At FLM chromatin, the histone H3K27 trimethylation is enhanced in response to increasing temperatures. Depletion of UBA2C weakens the response of FLM transcription and H3K27 trimethylation to temperature changes. UBA2C forms multiple puncta in the nucleus and the number of puncta increases with increasing temperatures. UBA2C contains a prion-like domain (PrLD) that is responsible for forming puncta in the nucleus in vivo. These results not only identify a previously unknown flowering-time regulator but also reveal the mechanism by which the regulator controls flowering time in response to temperature changes.
2021-10-28 | GSE165433 | GEO
Project description:Ambient temperature dependent flowering time is an important feature that is required for plants to reproduce in various environmental conditions. The rising global temperature poses a significant challenge to the growth and reproduction of plants. In Arabidopsis thaliana, FLM-β, a major splicing isoform of the flowering repressor gene FLOWERING LOCUS M, is down-regulated in response to increasing temperature and represents a critical mechanism for plants to respond to temperature changes. However, it is unknown how the transcript level of FLM-β is down-regulated. Here we identify an RRM domain-containing protein, UBA2C, as a previously uncharacterized flowering repressor by forward genetic screening. We demonstrate that UBA2C directly binds to FLM chromatin and facilitates FLM transcription predominantly by inhibiting the histone H3K27 trimethylation, a histone mark related to transcriptional repression. At FLM chromatin, the histone H3K27 trimethylation is enhanced in response to increasing temperatures. Depletion of UBA2C weakens the response of FLM transcription and H3K27 trimethylation to temperature changes. UBA2C forms multiple puncta in the nucleus and the number of puncta increases with increasing temperatures. UBA2C contains a prion-like domain (PrLD) that is responsible for forming puncta in the nucleus in vivo. These results not only identify a previously unknown flowering-time regulator but also reveal the mechanism by which the regulator controls flowering time in response to temperature changes.
2021-10-28 | GSE165432 | GEO
Project description:Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment. Compared to the control of flowering before and after winter by the vernalization and day length pathways, mechanisms that delay or promote flowering during a transient cool or warm period, especially during spring, are less well known. Due to global warming, understanding this ambient temperature pathway has become increasingly important. FLOWERING LOCUS M (FLM) is one critical flowering regulator of this pathway in Arabidopsis thaliana. We identified the Arabidopsis accession Kil-0 as an early flowering strain when compared to the common reference accession Col-0. Genetic mapping of this trait identified a causative region of around 31 kb at the bottom of chromosome one. Within this region, only FLOWERING LOCUS M (FLM) was expressed at a significantly lower level in Kil-0 when comparing RNA-seq (RNA sequencing) data from 10-day old Kil-0 and Col-0 plants grown at 21C. Furthermore, FLM was also the gene with the greatest reduction in gene expression between Kil-0 and Col-0 when we specifically analyzed 267 genes with a role in flowering time regulation what strongly suggested that FLM is the major locus that results in accelerated flowering in Kil-0.
2015-08-28 | E-MTAB-4473 | biostudies-arrayexpress
Project description:Two Arabidopsis thaliana splicing factor [AtU2AF65 isoforms (AtU2AF65a and AtU2AF65b)] mutants displayed the opposite flowering phenotypes. To assay the RNA processing including alternative splicing and pre-mRNA splicing of target genes of this protein in Arabidopsis, the 7-day seedlings (shoot apices) of wild type atu2af65a and atu2af65b mutants were used for RNA-Seq.
2023-05-01 | E-MTAB-12648 | biostudies-arrayexpress
Project description:Plants developed a plasticity to environmental conditions, such as temperature, 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 epigenetic mutants, sdg8-2 and sdg26-1 using an RNA-seq approach.
2017-05-10 | GSE85280 | GEO
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.
2017-05-10 | GSE85279 | 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:This study investigates extent and functional significance of alternative splicing in Arabidopsis thaliana defense against the bacterial pathogen Pseudomonas syringae pv tomato (Pst). We have provided a detailed characterization of the Arabidopsis thaliana transcriptional response to Pseudomonas syringae infection in both susceptible and resistant hosts. We carried out two independent inoculation experiments (biological replicates) for each treatment. Col-0 is susceptible to virulent Pst DC3000 but has a functional RPS4 resistance gene effective against DC3000 expressing AvrRps4
2013-03-06 | E-MTAB-4450 | biostudies-arrayexpress