GEO DataSets

(Submitter supplied) DNA methylation is an epigenetic mark that is associated with transcriptional repression of transposable elements and protein coding genes. Conversely, transcriptionally active regulatory regions are strongly correlated with histone 3 lysine 4 di- and trimethylation (H3K4m2/3). We previously showed that Arabidopsis thaliana plants with mutations in the H3K4m2/m3 demethylase JUMONJI 14 (JMJ14) exhibit a mild reduction in RNA-directed DNA methylation (RdDM) that is associated with an increase in H3K4m2/m3 levels. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL13222

34 Samples

Download data: WIG

(Submitter supplied) The small RNA mediated DNA methylation (RdDM) is highly elaborated in Arabidopsis as an important epigenetic pathway controls expression of genes and multiple developmental processes. RDR2 and DCL3 are necessary factors to the 24-nt siRNA biogenesis and the RdDM pathway. Here, we find that IBM1 (increase in BONSAI methylation 1), a conserved JmjC family histone demethylase, could directly associated with the chromatin of RDR2 and DCL3. more...

Organism:

Arabidopsis thaliana

Type:

Other; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

Platforms:

GPL10686 GPL10689

12 Samples

Download data: CALLS, GFF, PAIR

(Submitter supplied) Investigation of genome-wide expression in the mutant of histone H3K9 methyltransferase KRYPTONITE (KYP) or DNA methyltransferase CHROMOMETHYLASE3 (CMT3) in Arabidopsis. These mutants showed decrease in H3K9 methylation and DNA methylation levels, and transcriptional activation at transposons and repeats. Using NimbleGen DNA microarray, global pattern of expression of genes and transposons were examined in these mutants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL10689

6 Samples

Download data: CALLS, PAIR

(Submitter supplied) In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Despites the conservation and importance in the genome integrity, mechanisms to exclude H3K9m from active genes remained largely unexplored. Here we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation); loss-of-function ibm1 mutation caused ectopic H3K9me in thousands of genes, which accompanies genic DNA methylation at non-CG sites. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10686

6 Samples

Download data: GFF, PAIR

(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:

GPL11221 GPL13222

19 Samples

Download data: TXT

(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

(Submitter supplied) Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: WIG

(Submitter supplied) Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7143

6 Samples

Download data: PAIR

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

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by high throughput sequencing

Platforms:

GPL7143 GPL13222

8 Samples

Download data: PAIR, WIG

(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

(Submitter supplied) Functional genomic states are maintained by reinforcing chromatin interactions that exclude the components of other states. Plant heterochromatin features methylation of histone H3 at lysine 9 (H3K9me) and extensive DNA methylation. However, DNA methylation is also catalyzed by a mostly euchromatic small RNA-directed pathway (RdDM) thought to seek H3K9me. How RdDM is excluded from H3K9me-rich heterochromatin is unclear. 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

Platforms:

GPL19580 GPL21785

62 Samples

Download data: BW, GFF

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL23157 GPL21785

28 Samples

Download data: BW, CGMAP

(Submitter supplied) Histone deacetylases (HDAs) are evolutionally conserved enzymes and often form a multiprotein complex with histone Lysine-Specific Demethylase 1 (LSD1) to play central roles in epigenetic silencing in yeast and animals. In Arabidopsis, either HDA6 or LSD1-LIKE 1 and 2 (LDL1/2) are known to silence transposable element (TE), but their joint effect remains unexplored. Here, we revealed the individual and joint effects of HDA6 and LDL1/2 carefully by examining the transcriptomes, the genome wide distribution of H3Ac, H3K4me2, and DNA methylation in wildtype and mutants (hda6, ldl1/2 and hda6/ldl1/2). more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21785

12 Samples

Download data: BW

(Submitter supplied) Histone deacetylases (HDAs) are evolutionally conserved enzymes and often form a multiprotein complex with histone Lysine-Specific Demethylase 1 (LSD1) to play central roles in epigenetic silencing in yeast and animals. In Arabidopsis, either HDA6 or LSD1-LIKE 1 and 2 (LDL1/2) are known to silence transposable element (TE), but their joint effect remains unexplored. Here, we revealed the individual and joint effects of HDA6 and LDL1/2 carefully by examining the transcriptomes, the genome wide distribution of H3Ac, H3K4me2, and DNA methylation in wildtype and mutants (hda6, ldl1/2 and hda6/ldl1/2). more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23157

8 Samples

Download data: CGMAP

(Submitter supplied) Histone deacetylases (HDAs) are evolutionally conserved enzymes and often form a multiprotein complex with histone Lysine-Specific Demethylase 1 (LSD1) to play central roles in epigenetic silencing in yeast and animals. In Arabidopsis, either HDA6 or LSD1-LIKE 1 and 2 (LDL1/2) are known to silence transposable element (TE), but their joint effect remains unexplored. Here, we revealed the individual and joint effects of HDA6 and LDL1/2 carefully by examining the transcriptomes, the genome wide distribution of H3Ac, H3K4me2, and DNA methylation in wildtype and mutants (hda6, ldl1/2 and hda6/ldl1/2). more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23157

8 Samples

Download data: BW

(Submitter supplied) Transgene loci that spontaneously undergo RNA silencing have been instrumental to decipher RNA silencing pathways in plants. In contrast, transgene loci that are stably expressed have been poorly characterized. Here we show that stably expressed transgene loci epigenetically differ from endogenous genes. Impairing the histone H3K4me3 demethylase JMJ14 increases DNA methylation at stably expressed transgene loci but not at endogenous genes, whereas impairing the histone H3K9me2 demethylase IBM1 increases DNA methylation at endogenous genes, but decreases DNA methylation at stably expressed transgene loci. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL28290

7 Samples

Download data: WIG

(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:

GPL13222

15 Samples

Download data: TXT

(Submitter supplied) RNA-directed DNA methylation (RdDM) is a transcriptional silencing mechanism mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1a (TOP1a) was able to de-repress LUCL by reducing its DNA methylation and H3K9 dimethylation (H3K9me2) levels. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

5 Samples

Download data: TXT

(Submitter supplied) RNA-directed DNA methylation (RdDM) is a transcriptional silencing mechanism mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α) was able to de-repress LUCL by reducing its DNA methylation and H3K9 dimethylation (H3K9me2) levels. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

10 Samples

Download data: TXT