Similar studies for GEO DataSets (Select 200127992) - GEO DataSets

Select item 2001279921.

The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA methylation pathway in sporophyte and pollen development [small RNA]

(Submitter supplied) RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL17639
6 Samples

Download data: TXT

Series

Accession:: GSE127992

ID:: 200127992

PubMed Similar studies SRA Run Selector

Select item 2001279932.

The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA methylation pathway in sporophyte and pollen development

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

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:: GPL17639 GPL13222
12 Samples

Download data: TXT

Series

Accession:: GSE127993

ID:: 200127993

PubMed Similar studies

Select item 2001279913.

The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA methylation pathway in sporophyte and pollen development [RNA-seq]

(Submitter supplied) RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13222
6 Samples

Download data: TXT

Series

Accession:: GSE127991

ID:: 200127991

PubMed Similar studies SRA Run Selector

Select item 2000576904.

Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana

(Submitter supplied) The poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13222
16 Samples

Download data: TXT

Series

Accession:: GSE57690

ID:: 200057690

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000797805.

Comparing the targets of distinct RNA Directed DNA Methylation mechanisms in Arabidopsis thaliana

(Submitter supplied) The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wt Col ecotype of Arabidopsis thaliana. In plants mutant for the SWI/SNF2 histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Activated TEs go through additional non-canonical forms of RdDM. more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platforms:: GPL13222 GPL11221
19 Samples

Download data: TXT

Series

Accession:: GSE79780

ID:: 200079780

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000797466.

Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

(Submitter supplied) The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wild-type reference strains of Arabidopsis thaliana. In plants mutant for the SWI/SNF histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Transcriptionally activated TEs go through additional non-canonical forms of RdDM that are dependent on RNA Polymerase II expression. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL19580
21 Samples

Download data: TSV, TXT

Series

Accession:: GSE79746

ID:: 200079746

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000417557.

Arabidopsis small RNAs associated with RDR6-dependent RNA-directed DNA Methylation

(Submitter supplied) Background: The majority of plant transposable elements (TEs) are found in a silenced state that is epigenetically propagated by the maintenance of symmetrical DNA methylation. TE methylation is established and reinforced by a mechanism of RNA-dependent DNA methylation, which is dependent on transcription of the PolIV RNA polymerase. Recently, a pathway has been described that initiates de novo DNA methylation dependent on components of the RNAi post-transcriptional silencing pathway, independent of PolIV. more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL11221
4 Samples

Download data: TXT

Series

Accession:: GSE41755

ID:: 200041755

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000488218.

Target specificity amongst canonical nuclear poly(A) polymerases in plants modulates organ growth and pathogen response

(Submitter supplied) Polyadenylation of pre-mRNAs is critical for efficient nuclear export, stability and translation of the mature mRNAs, and thus for gene expression. The bulk of pre-mRNAs are processed by canonical nuclear poly(A) polymerase (PAPS). Both vertebrate and higher-plant genomes encode more than one isoform of this enzyme, and these are co-expressed in different tissues. However, in neither case is it known whether the isoforms fulfil different functions or polyadenylate distinct subsets of pre-mRNAs. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL7299
8 Samples

Download data: TXT

Series

Accession:: GSE48821

ID:: 200048821

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2002075099.

Transcriptomic analyses to estimated poly(A)-tail lengths in paps1-1 mutant pollen tubes

(Submitter supplied) Polyadenylation of mRNAs is critical for their export from the nucleus, stability and efficient translation. The Arabidopsis thaliana genome encodes three isoforms of canonical nuclear poly(A) polymerase (PAPS) that redundantly polyadenylate the bulk of pre-mRNAs. However, their distinct mutant phenotypes and transcriptome studies have indicated that subsets of pre-mRNAs are preferentially polyadenylated by either PAPS1 or the two very similar PAPS2 and PAPS4 proteins. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19580
16 Samples

Download data: TAB

Series

Accession:: GSE207509

ID:: 200207509

PubMed Similar studies

Select item 20020728510.

Transcriptomic analyzes of paps1 pollen tube/style complexes

(Submitter supplied) Polyadenylation of mRNAs is critical for their export from the nucleus, stability and efficient translation. The Arabidopsis thaliana genome encodes three isoforms of canonical nuclear poly(A) polymerase (PAPS) that redundantly polyadenylate the bulk of pre-mRNAs. However, their distinct mutant phenotypes and transcriptome studies have indicated that subsets of pre-mRNAs are preferentially polyadenylated by either PAPS1 or the two very similar PAPS2 and PAPS4 proteins. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13222
6 Samples

Download data: TAB

Series

Accession:: GSE207285

ID:: 200207285

PubMed Similar studies

Select item 20005719111.

Small RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes

(Submitter supplied) Background: The small RNAs that Transposable Elements generate are vastly different when they are transcriptionally silenced compared to when they are transcriptionally activated. We performed the deep sequencing of small RNAs in a number of small RNA biogenesis mutants in both Transposable Element-silenced and Transposable Element-active epigenome backgrounds. Results: We found that Transposable Elements generate large amounts of 21-22nt siRNAs only when they are transcriptionally active. more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL13222
22 Samples

Download data: TXT

Series

Accession:: GSE57191

ID:: 200057191

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20001830212.

Deep sequencing of small RNAs in the trasngenic wild type plant and the IWR1-type transcription factor mutant, dms4

(Submitter supplied) Full title: Deep sequencing of small RNAs in the trasngenic wild type plant (contains trigger and silencer transgenes) and the IWR1-type transcription factor mutant, dms4 RNA-directed DNA methylation (RdDM) in plants requires two RNA polymerase II (PolII)-related RNA polymerases named PolIV and PolV. A genetic screen designed to reveal factors important for RdDM in a developmental context in Arabidopsis identified DEFECTIVE IN MERISTEM SILENCING 4 (DMS4). more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL9302
2 Samples

Download data

Series

Accession:: GSE18302

ID:: 200018302

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20013361813.

Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes

(Submitter supplied) Canonically, Arabidopsis RNA Polymerase IV (Pol IV) is known to produce heterochromatic small RNAs (typically 23-24 nucleotide in length) that maintain silencing of transposable elements (TEs). In contrast, when TEs are transcriptionally activated and produce Pol II transcripts, these transcripts are degraded into 21-22 nt small RNAs (sRNAs) known to participate in post transcriptional gene silencing. more...

Organism:: Arabidopsis thaliana

Type:: Other; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:: GPL17639 GPL19580 GPL21785
19 Samples

Download data: TSV

Series

Accession:: GSE133618

ID:: 200133618

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012475014.

Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [ChIP-seq]

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:: Arabidopsis thaliana

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21785
56 Samples

Download data: BW

Series

Accession:: GSE124750

ID:: 200124750

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012474915.

Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [small RNA-seq]

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platforms:: GPL13222 GPL17639
39 Samples

Download data: BW

Series

Accession:: GSE124749

ID:: 200124749

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012474716.

Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [RNA-seq]

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21785
40 Samples

Download data: TXT

Series

Accession:: GSE124747

ID:: 200124747

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012474617.

Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [WGBS]

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platforms:: GPL21785 GPL13222
45 Samples

Download data: BW

Series

Accession:: GSE124746

ID:: 200124746

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012474418.

Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [BS-PCR-seq]

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platforms:: GPL13222 GPL17639
66 Samples

Download data: TXT

Series

Accession:: GSE124744

ID:: 200124744

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012454619.

Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing