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Next generation sequencing comparing RNA-seq data from Arabidopsis Col-0 wild type and splicing factor mutant prp8a-14

ABSTRACT: Purpose: Identify alternative splicing events and changes to transcript expression levels

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE182779 | GEO | 2022/07/05

REPOSITORIES: GEO

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Alternative splicing in Col-0 and sc35-scl mutant in Arabidopsis tlianaha

Project description:Serine/arginine-rich (SR) proteins are important splicing factors which play significant roles in spliceosome assembly and splicing regulation. However, little is known regarding their biological functions in plants. Here, we analyzed the phenotypes of mutants upon depleting different subfamilies of Arabidopsis SR proteins. We found that loss of the functions of SC35 and SC35-like (SCL) proteins cause pleiotropic changes in plant morphology and development, including serrated leaves, late flowering, shorter roots and abnormal silique phyllotaxy. Using RNA-seq, we found that SC35 and SCL proteins play roles in the pre-mRNA splicing. Motif analysis revealed that SC35 and SCL proteins preferentially bind to a specific RNA sequence containing the AGAAGA motif. In addition, the transcriptions of a subset of genes are affected by the deletion of SC35 and SCL proteins which interact with NRPB4, a specific subunit of RNA polymerase II. The splicing of FLOWERING LOCUS C (FLC) intron1 and transcription of FLC were significantly regulated by SC35 and SCL proteins to control Arabidopsis flowering. Therefore, our findings provide mechanistic insight into the functions of plant SC35 and SCL proteins in the regulation of splicing and transcription to maintain the proper expression of genes and development.

2017-01-26 | GSE93910 | GEO

Next generation sequencing comparing RNA-seq data from Arabidopsis Col-0 wild type and splicing factor mutant prp8a-14

Project description:Next generation sequencing comparing RNA-seq data from Arabidopsis Col-0 wild type and splicing factor mutant prp8a-14

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Transriptome analysis of alternative splicing under heat stress condition in atcyp18-2 mutant compared to Wild type (Col-0) of Arabidopsis

Project description:To investigate whether the observed changes in pre-mRNA splicing led to AtCYP18-2 depletion, we conducted RNA-sequencing to analyse the quantitative profiling of alternative splicing

2021-02-16 | GSE166755 | GEO

mRNA-seq data of 14 days old Arabidopsis seedlings in Col-0 and At rz-1b At rz-1c double mutant

Project description:Nuclear-localized RNA binding proteins are involved in various aspects of RNA metabolism, which in turn modulates gene expression. However, the functions of nuclear-localized RNA binding proteins in plants are poorly understood. Here we report the functions of two proteins containing RNA recognition motifs, At RZ-1B and At RZ-1C, in Arabidopsis. At RZ-1B and At RZ-1C were localized to nuclear speckles and interacted with a spectrum of serine/arginine-rich (SR) proteins through their C-termini. At RZ-1C preferentially bound to purine-rich RNA sequences in vitro through its N-terminal RNA recognition motif. Disrupting the RNA-binding activity of At RZ-1C with SR proteins through over-expression of the C-terminus of At RZ-1C conferred defective phenotypes similar to those observed in At rz-1b/At rz-1c double mutants, including delayed seed germination, reduced stature, and serrated leaves. Loss of function of At RZ-1B and At RZ-1C was accompanied by defective splicing of many genes and global perturbation of gene expression. In addition, we found that At RZ-1C directly targeted FLC, promoting efficient splicing of FLC introns and likely also repressing FLC transcription. Our findings highlight the critical role of At RZ-1B/1C in regulating RNA splicing, gene expression, and many key aspects of plant development via interaction with proteins including SR proteins.

2015-12-15 | GSE75959 | GEO

mRNA-seq data of 14 days old Arabidopsis seedlings in Col-0 and At rz-1b At rz-1c double mutant

2015-12-15 | E-GEOD-75959 | biostudies-arrayexpress

Arabidopsis thaliana strain:Col-0 | cultivar:Col-0 Mutant Line #14

Project description:Arabidopsis thaliana strain:Col-0 | cultivar:Col-0 Mutant Line #14 Genome sequencing

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Mapping QTLs for 15 morpho-metric traits in <i>Arabidopsis thaliana</i> using Col-0 × Don-0 population.

Project description:Genome wide quantitative trait loci (QTL) mapping was conducted in Arabidopsis thaliana using F2 mapping population (Col-0 × Don-0) and SNPs markers. A total of five linkage groups were obtained with number of SNPs varying from 45 to 59 per linkage group. The composite interval mapping detected a total of 36 QTLs for 15 traits and the number of QTLs ranged from one (root length, root dry biomass, cauline leaf width, number of internodes and internode distance) to seven (for bolting days). The range of phenotypic variance explained (PVE) and logarithm of the odds ratio of these 36 QTLs was found be 0.19-38.17% and 3.0-6.26 respectively. Further, the epistatic interaction detected one main effect QTL and four epistatic QTLs. Five major QTLs viz. Qbd.nbri.4.3, Qfd.nbri.4.2, Qrdm.nbri.5.1, Qncl.nbri.2.2, Qtd.nbri.4.1 with PVE > 15.0% might be useful for fine mapping to identify genes associated with respective traits, and also for development of specialized population through marker assisted selection. The identification of additive and dominant effect QTLs and desirable alleles of each of above mentioned traits would also be important for future research.

| S-EPMC7196571 | biostudies-literature

Next Generation Sequencing of Wild Type (Col-0) , LNJ overexpressor and jazD Transcriptomes in Arabidopsis thaliana

Project description:Plants were grown for 21 days under LD conditions and RNA was extracted and sequenced

2020-09-25 | GSE155487 | GEO

Artificial Autopolyploidization Modifies the Tricarboxylic Acid Cycle and GABA Shunt in Arabidopsis thaliana Col-0.

Project description:Autopolyploidy is a process whereby the chromosome set is multiplied and it is a common phenomenon in angiosperms. Autopolyploidy is thought to be an important evolutionary force that has led to the formation of new plant species. Despite its relevance, the consequences of autopolyploidy in plant metabolism are poorly understood. This study compares the metabolic profiles of natural diploids and artificial autotetraploids of Arabidopsis thaliana Col-0. Different physiological parameters are compared between diploids and autotetraploids using nuclear magnetic resonance (NMR), elemental analysis (carbon:nitrogen balance) and quantitative real-time PCR (qRT-PCR). The main difference between diploid and autotetraploid A. thaliana Col-0 is observed in the concentration of metabolites related to the tricarboxylic acid cycle (TCA) and ?-amino butyric acid (GABA) shunt, as shown by multivariate statistical analysis of NMR spectra. qRT-PCR shows that genes related to the TCA and GABA shunt are also differentially expressed between diploids and autotetraploids following similar trends as their corresponding metabolites. Solid evidence is presented to demonstrate that autopolyploidy influences core plant metabolic processes.

| S-EPMC4876396 | biostudies-literature

Bisulfite (methylome) sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; Col-0 grafted on Col-0; msh1 mutant; dcl2,3,4,msh1 quadruple mutant in Arabidopsis [msh1_graft_BS-seq]

Project description:Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1); on Col-0 (Col-0/Col-0). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the bisulfite sequencing (methylome). Tissue from the msh1 mutant and dcl2,3,4,msh1 quadruple mutants used as rootstocks was similarly collected at the bolting stage and used for the bisulfite sequencing.

2020-09-20 | GSE152564 | GEO

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