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Links from GEO DataSets

Items: 20

1.

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
2.

Structural Variant of a Tandem Repeat-containing Silencer Locus Reveals Distinct Pol II and Pol IV-dependent Pathways of siRNA Biogenesis

(Submitter supplied) We used a two-component transgene system to study the RNA-dependent DNA methylation (RdDM) and transcriptional gene silencing (TGS) in Arabidopsis. By profiling the small RNA population in  mutants defected in RdDM or RNA polymerase II-transcribed trigger for generating silencing siRNA, we investigated how repetitive loci such as tandem repeats were regulated transcriptionally through the action of RNA polymerase IV.
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13222
6 Samples
Download data: TXT
Series
Accession:
GSE47852
ID:
200047852
3.

Bisulfite-Seq profiling of wild-type Arabidopsis with two-component transgene silencing (T+S) system

(Submitter supplied) In plants, RNA polymerase II (Pol II) transcription of inverted DNA repeats produces hairpin RNAs that are processed by several DICER-LIKE enzymes into siRNAs that are 21-24-nt in length. When targeted to transcriptional regulatory regions, the 24-nt size class can induce RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS). In a forward genetic screen to identify mutants defective in RdDM of a target enhancer leading to TGS of a downstream GFP reporter gene in Arabidopsis thaliana, we recovered a structurally mutated silencer locus, named SΔ35S, in which the 35S promoter driving transcription of an inverted repeat of target enhancer sequences had been specifically deleted. more...
Organism:
Arabidopsis thaliana
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13222
1 Sample
Download data: TXT
Series
Accession:
GSE47453
ID:
200047453
4.

Dicer-independent RNA-directed DNA methylation in Arabidopsis [small RNA-seq 2]

(Submitter supplied) Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of dcl2/3/4/nrpd1 and nrpd1 mutants
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13222
2 Samples
Download data: BEDGRAPH
Series
Accession:
GSE71672
ID:
200071672
5.

Dicer-independent RNA-directed DNA methylation in Arabidopsis [small RNA-seq 1]

(Submitter supplied) Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of dcl2/3/4, dcl1/2/3/4 and WT
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13222
3 Samples
Download data: BEDGRAPH
Series
Accession:
GSE70913
ID:
200070913
6.

Dicer-independent RNA-directed DNA methylation in Arabidopsis [methylC-seq]

(Submitter supplied) Using MethylC-Seq to provide single-base resolution of DNA methylation status in Col-0 and some RdDM mutants
Organism:
Arabidopsis thaliana
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13222
23 Samples
Download data: WIG
Series
Accession:
GSE70912
ID:
200070912
7.

Pol-IV dependent transcripts in Arabidopsis

(Submitter supplied) small RNA, PATH and mRNA libraries were made to characterize Col and various small RNA biogenesis mutants.
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17639
42 Samples
Download data: PDF, TXT, WIG, XLSX
Series
Accession:
GSE61439
ID:
200061439
8.

Polymerase IV Plays a Crucial Role in Pollen Development in Capsella

(Submitter supplied) In Arabidopsis thaliana, DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA (sRNA) transcripts. These transcripts are processed by DICER-LIKE3 into 24-nt small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nt epigenetically activated siRNAs (easiRNAs), which likely silence TEs via post-transcriptional mechanisms. more...
Organism:
Arabidopsis thaliana; Capsella rubella
Type:
Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing
Platforms:
GPL25199 GPL17639 GPL19580
32 Samples
Download data: TXT
Series
Accession:
GSE136847
ID:
200136847
9.

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

(Submitter supplied) MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. more...
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL17639
16 Samples
Download data: BED, BEDGRAPH, TXT
Series
Accession:
GSE129744
ID:
200129744
10.

Detection of Pol IV-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis

(Submitter supplied) 24 nucleotide siRNAs are central players in RNA-directed DNA methylation (RdDM), a process that establishes DNA methylation at transposable elements to ensure genome stability. The plant-specific RNA polymerase IV (Pol IV) is required for siRNA biogenesis and is thought to transcribe RdDM loci to produce primary transcripts that serve as precursors to siRNAs. Yet, no such transcripts have ever been reported. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13222
36 Samples
Download data: WIG
Series
Accession:
GSE57215
ID:
200057215
11.

Maize (Zea mays) leaf transcriptome analysis under abiotic stress in wild type and RNA Polymerase IV mutant

(Submitter supplied) Plants have developed complex mechanisms to respond and adapt to abiotic stresses, coupling elaborate modulation of gene expression together with the preservation of genome stability. Epigenetic mechanisms - DNA methylation, chromatin modifications and non coding RNAs - were shown to play a fundamental role in stress-induced gene regulation and may also result in genome destabilization, with the activation and/or the transcription of silenced transposons and retroelements, causing genome rearrangements and novel gene expression patterns. more...
Organism:
Zea mays
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15463
32 Samples
Download data: GTF, TXT
Series
Accession:
GSE71046
ID:
200071046
12.

The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice

(Submitter supplied) RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of Pol V, a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long non-coding RNAs. Pol V influences the accumulation of 24-nt siRNAs in a locus-specific manner. more...
Organism:
Oryza sativa
Type:
Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL24468 GPL24983
8 Samples
Download data: TDF
Series
Accession:
GSE158711
ID:
200158711
13.

The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice [Bisulfite-Seq]

(Submitter supplied) RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of Pol V, a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long non-coding RNAs. Pol V influences the accumulation of 24-nt siRNAs in a locus-specific manner. more...
Organism:
Oryza sativa
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24468
5 Samples
Download data: TDF
Series
Accession:
GSE158710
ID:
200158710
14.

The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice [ncRNA-Seq]

(Submitter supplied) RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of Pol V, a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long non-coding RNAs. Pol V influences the accumulation of 24-nt siRNAs in a locus-specific manner. more...
Organism:
Oryza sativa
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL24983
3 Samples
Download data: TDF
Series
Accession:
GSE158709
ID:
200158709
15.

High-throughput sequencing of Pol IV and RDR2 transcripts, and their DCL3-diced products, generated from an M13mp18 (+) strand DNA template

(Submitter supplied) In plants, the biogenesis of 24 nt and 23 nt small interfering RNAs (siRNAs) requires NUCLEAR RNA POLYMERASE IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). We show that single-stranded M13 bacteriophage DNA can be used as a template for siRNA synthesis in vitro. Deep sequencing of RNAs produced from the in vitro reactions of Pol IV, RDR2 and DCL3 shows that Pol IV transcribes the DNA into first-strand RNAs which RDR2 then uses as templates to synthesize complementary second strands. more...
Organism:
synthetic construct
Type:
Other
Platform:
GPL19424
4 Samples
Download data: TXT
Series
Accession:
GSE126086
ID:
200126086
16.

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
17.

Small RNA-seq of ago4 null and slicing-defective mutant in Arabidopsis

(Submitter supplied) To investigate the effect of AGO4 upon small RNA accumulation in Arabidopsis, we analyzed small RNA accumulation in ago4, ago4/ago6/ago9 triple mutant, stable transgenic lines expressing wild-type AGO4 and slicing-defective AGO4 in ago4 and ago4/ago6/ago9 background.
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17639
21 Samples
Download data: TXT
Series
Accession:
GSE87333
ID:
200087333
18.

Arabidopsis thaliana Col-0 inflorescence small RNAs

(Submitter supplied) Small RNA sequences from Arabidopsis thaliana Col-0 inflorescence tissues of three biological replicates. The data were analyzed to identify non-templated nucleotides in Arabidopsis small RNAs.
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17639
3 Samples
Download data: TXT
Series
Accession:
GSE79119
ID:
200079119
19.

Functional analysis of the Pol IV DeCL domain

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL19580
14 Samples
Download data: TXT
Series
Accession:
GSE95825
ID:
200095825
20.

Assessment of the Pol IV largest subunit, NRPD1, DeCL domain deletion construct to rescue Pol IV-dependent siRNAs in the nrpd1-3 mutant (sRNA).

(Submitter supplied) The Arabidopsis thaliana multi-subunit RNA Polymerase IV largest subunit DeCL domain was functionally assessed with an NRPD1 DeCL domain deletion construct.
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL19580
8 Samples
Download data: TXT
Series
Accession:
GSE95824
ID:
200095824
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