Similar studies for GEO DataSets (Select 200021323) - GEO DataSets

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Items: 20

Select item 2000213231.

Protein arginine methyltransferase AtPRMT5 is involved in pre-mRNA splicing in Arabidopsis thaliana

(Submitter supplied) In this study, we analyzed the Arabidopsis homologue of PRMT5, AtPRMT5’s function in RNA processing. RNA-seq analyses revealed that AtPRMT5 is involved in a subset of pre-mRNA splicing. Several RNA processing factors involved in regulating flowering time were validated that the corresponding intron retention surely exists in atprmt5 mutants. AtSm proteins can also be methylated by AtPRMT5 in vitro and in vivo, which may be the reasons for the pre-mRNA splicing defects in atprmt5. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL10272
2 Samples

Download data: BEDGRAPH

Series

Accession:: GSE21323

ID:: 200021323

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000626112.

Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5

(Submitter supplied) In this study, we analyzed the pre-mRNA splicing status in wild-type Col, atprmt5 mutants, and two atprmt5 suppressors (m90 and s215). RNA-seq analyses revealed that m90 and s215 can partially rescue the pre-mRNA splicing defects in atprmt5 mutants. Further study showed that m90 and s215 were identified in the highly conserved pre-mRNA splicing factor 8 (AtPrp8) and demonstrated that Prp19C/NTC complex failed to be assembled into U5 snRNP to form activated spliceosome in atprmt5 mutants, while restored in the suppressor. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13222
4 Samples

Download data: BW, TXT

Series

Accession:: GSE62611

ID:: 200062611

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Select item 2000188083.

A methyl transferase links the circadian clock to the regulation of alternative splicing

(Submitter supplied) Study on differential gene expression and splicing between wildtype and clock mutants. This study is part of a comparative analysis of the role of Protein Methyltransferase 5 in the regulation of transcriptional and post-transcriptional processes simultaneously in Arabidopsis and Drosophila. Circadian rhythms allow organisms to time biological processes to the most appropriate phases of the day/night cycle1. more...

Organism:: Arabidopsis thaliana; Drosophila melanogaster

Type:: Expression profiling by array; Expression profiling by genome tiling array

Platforms:: GPL198 GPL1979 GPL6882
18 Samples

Download data: CEL

Series

Accession:: GSE18808

ID:: 200018808

Select item 2000263984.

Arabidopsis floral initiator SKB1 confers high salt tolerance by regulating transcription and pre-mRNA splicing through altering histone H4R3 and small nuclear ribonucleoprotein LSM4 methylation

(Submitter supplied) This study examines how histone modification confers salt stress in Arabidopsis. The floral initiator SKB1 is found to mediate the plant’s response to salt stress by altering the methylation status of histone H4R3 and of the small nuclear ribonucleoprotein (snRNP) LSM4, and thereby affecting the expression of stress-responsive genes.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL11375
6 Samples

Download data

Series

Accession:: GSE26398

ID:: 200026398

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000620245.

Genome-wide analysis of the prmt5 and prmt4a;4b mutant transcriptomes

(Submitter supplied) The goal of this study was to compare the transcriptional profile (RNA-seq) of prmt5 and prmt4a;4b Arabidopsis mutants with their respective wild type plants grown under continous light conditions

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19080
9 Samples

Download data: XLSX

Series

Accession:: GSE62024

ID:: 200062024

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Select item 2000858836.

SPLICING FACTOR FOR PHYTOCHROME SIGNALING promotes photomorphogenesis by regulating alternative splicing in Arabidopsis

(Submitter supplied) Purpose: The goals of this study are to compare the transcriptome profiling and alternative splicing (AS) profiling between Col-0 wild type and SFPS knockout mutant (sfps-2) through RNA-seq to determine the molecular mechanisms of how splicing factor SFPS regulates photomorphogenesis in Arabidopsis. Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified 1495 differentially expressed genes between Col-0 and mutant dark samples; 1361 differentially expressed genes between Col-0 and mutant red light treated samples; 4291 differentially expressed genes between Col-0 dark and red light treated samples; and 4479 differentially expressed genes between mutant dark and red light treated samples. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21179
12 Samples

Download data: TXT, XLSX

Series

Accession:: GSE85883

ID:: 200085883

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Select item 2000795237.

Arabidopsis Messenger RNA N6-methyladenosine Demethylation Regulates Plant Development

(Submitter supplied) N6-methyladenosine (m6A) is the most abundant internal modification in the messenger RNA (mRNA) of all higher eukaryotes. This modification has been shown to be reversible in mammals; it is installed by a methyltransferase heterodimer complex of METTL3 and METTL14 bound with WTAP, and reversed by iron(II)- and α-ketoglutarate-dependent demethylases FTO and ALKBH5. This modification exhibits significant functional roles in various biological processes. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL17639
8 Samples

Download data: TXT

Series

Accession:: GSE79523

ID:: 200079523

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Select item 2000481148.

Pre-mRNA splicing factor atsf1-2 mutant seedlings

(Submitter supplied) Analysis of atsf1-2 mutant seedlings for pre-mRNA splicing defect. The atsf1-2 mutant is a homozygous T-DNA insertion line isolated from a SALK line, SALK_062177. Results identify transcripts with altered alternative splicing pattern in the atsf1-2 mutant. We used microarrays to examine the transcriptome profile in the atsf1-2 mutant and identified genes of which transcript levels were changed significantly.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL198
6 Samples

Download data: CEL, CHP

Series

Accession:: GSE48114

ID:: 200048114

Select item 2000759599.

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

(Submitter supplied) 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. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9302
4 Samples

Download data: BW

Series

Accession:: GSE75959

ID:: 200075959

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Select item 20006528710.

Arabidopsis thaliana cao mutant alternative splicing exploration by RNAseq

(Submitter supplied) The early flowering Arabidopsis cäö mutant is defective in the BRR2a helicase involved in splicing. In order to get some explanation about the phenotype, we compared the expression profiles of wt and mutant with RNA-seq. In addtion, the same RNA-seq data was used to measure the extent of intron retention in the cäö mutant

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17311
6 Samples

Download data: TSV

Series

Accession:: GSE65287

ID:: 200065287

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20003905111.

Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein， regulates plant flowering by targeted alternative polyadenylation

(Submitter supplied) Alternative polyadenylation (APA) is a widespread mechanism for gene regulation and has been implicated in flowering, but the molecular basis governing the choice of a specific poly(A) site during the vegetative-to-reproductive growth transition remains unclear. Here we characterize HLP1, an hnRNP A/B protein as a novel regulator for pre-mRNA 3’ end processing in Arabidopsis. Genetic analysis reveals that HLP1 suppresses Flowering Locus C (FLC), a key repressor of flowering in Arabidopsis. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL9302 GPL13222
8 Samples

Download data: BED, WIG

Series

Accession:: GSE39051

ID:: 200039051

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Select item 20005189812.

Gene expression analysis of overexpression and loss-of-function at JUMONJI30

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL13970
8 Samples

Download data: PAIR

Series

Accession:: GSE51898

ID:: 200051898

Select item 20005189713.

Gene expression analysis of jmj30 jmj32 mutant grown at 29°C under long day conditions

(Submitter supplied) Analysis of loss-of-function mutants of JUMONJI30 (JMJ30) and JMJ32 in Arabidopsis thaliana (Col). JMJ30 and JMJ32 encode the histone demethylases that contain the catalytic JmjC domain. The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL13970
4 Samples

Download data: PAIR

Series

Accession:: GSE51897

ID:: 200051897

Select item 20005189614.

Gene expression analysis of 35S::JMJ30-HA overexpression transgenic lines grown at 22°C under long day conditions

(Submitter supplied) Analysis of overexpression of JMJ30 in Arabidopsis thaliana (Col). JMJ30 encode the histone demethylases that contain the catalytic JmjC domain. The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL13970
4 Samples

Download data: PAIR

Series

Accession:: GSE51896

ID:: 200051896

Select item 20004441715.

Whole genome bisulfite sequencing of rdm16ros1, ros1, nrpd1ros1 mutants and C24 wild-type

(Submitter supplied) Using whole genome bisulfite sequencing to provide single-base resolution of DNA methylation status in rdm16ros1, ros1, nrpd1ros1 mutants and examine the effect of RDM16 on DNA methylation

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL13222
4 Samples

Download data: WIG

Series

Accession:: GSE44417

ID:: 200044417

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Select item 20012606416.

Global co-transcriptional splicing in Arabidopsis and the correlation with splicing regulation in mature RNAs

(Submitter supplied) RNA splicing and spliceosome assembly in eukaryotes occur mainly during transcription. However, co-transcriptional splicing has not yet been explored in plants. Here, we showed that in Arabidopsis thaliana, nearly all introns undergo co-transcriptional splicing and this occurs with higher efficiency for introns in protein-coding genes than for noncoding RNAs. Co-transcriptional splicing efficiency correlates with density of 19 epigenetic modifications. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23157
18 Samples

Download data: WIG

Series

Accession:: GSE126064

ID:: 200126064

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014031817.

Protein Arginine Methyltransferase 3 Fine-Tunes the Assembly/Disassembly of Pre-ribosomes to Repress Nucleolar Stress by Interacting with RPS2B in Arabidopsis

(Submitter supplied) Ribosome biogenesis, which takes place mainly in the nucleolus, involves coordinated expression of pre-ribosomal RNAs (pre-rRNAs) and ribosomal proteins, pre-rRNA processing, and subunit assembly with the aid of numerous assembly factors. Our previous study showed that the Arabidopsis thaliana protein arginine methyltransferase AtPRMT3 regulates pre-rRNA processing; however, the underlying molecular mechanism remains unknown. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17639
4 Samples

Download data: TXT

Series

Accession:: GSE140318

ID:: 200140318

PubMed Similar studies SRA Run Selector

Select item 20016342118.

Type I and II PRMTs Inversely Regulate Post-Transcriptional Intron Detention through

(Submitter supplied) Protein arginine methyltransferases (PRMTs) are required for the regulation of RNA processing factors. Type I PRMT enzymes catalyze mono- and asymmetric dimethylation; Type II enzymes catalyze mono- and symmetric dimethylation. To understand the specific mechanisms of PRMT activity in splicing regulation, we inhibited Type I and II PRMTs and probed their transcriptomic consequences. Using the newly developed Splicing Kinetics and Transcript Elongation Rates by Sequencing (SKaTER-seq) method, analysis of co-transcriptional splicing demonstrated that PRMT inhibition resulted in altered splicing rates. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL24676
96 Samples

Download data: BW, TXT

Series

Accession:: GSE163421

ID:: 200163421

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20011696419.

SmE1 is a functional subunit of the Arabidopsis Sm-ring that controls plant development and response to cold stress

(Submitter supplied) We report the role of SmE1 protein in the control of Arabidopsis development and tolerance to abiotic stresses. SmE1 controls gene expression reprogramming at the post-transcriptional level by promoting the splicing of pre-mRNA. This function is selectively achieve over selected transcripts depending on the stimulus nature.