Similar studies for GEO DataSets (Select 200038286) - GEO DataSets

Select item 2000382861.

DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis.

(Submitter supplied) The relationship between epigenetic marks on chromatin and the regulation of DNA replication is poorly understood. Mutation of the H3K27 methyltransferase genes, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, result in re-replication (repeated origin firing within the same cell cycle). Here we show that mutations that reduce DNA methylation act to suppress the re-replication phenotype of atxr5 atxr6 mutants. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:: GPL9302 GPL13222 GPL11221
43 Samples

Download data: TXT

Series

Accession:: GSE38286

ID:: 200038286

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000390972.

Dual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Mediates DNA Methylation in Plants

(Submitter supplied) DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2 and CMT3 stably associated with H3K9me2-containing nucleosomes. more...

Organism:: Arabidopsis thaliana

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

Platform:: GPL13222
2 Samples

Download data: TXT

Series

Accession:: GSE39097

ID:: 200039097

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000224113.

Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases

(Submitter supplied) Multiple pathways prevent DNA replication from occurring more than once per cell cycle. These pathways block re-replication by strictly controlling the activity of pre-replication complexes, which assemble at specific sites in the genome called origins. Here we show that mutations in the homologous histone 3 lysine 27 (H3K27) monomethyltransferases, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, lead to re-replication of specific genomic locations. The vast majority of these locations correspond to transposons and other repetitive and silent elements of the Arabidopsis genome. These sites also correspond to high levels of H3K27 monomethylation, and mutation of the catalytic SET domain is sufficient to cause the re-replication defect. Mutation of ATXR5 and ATXR6 also causes upregulation of transposon expression and has pleiotropic effects on plant development. These results uncover a novel pathway that prevents over-replication of heterochromatin in Arabidopsis.

Organism:: Arabidopsis thaliana

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

Platform:: GPL9302
12 Samples

Download data: TXT

Series

Accession:: GSE22411

ID:: 200022411

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000160714.

Loss of H3K27 monomethylation leads to DNA-methylation-independent release of gene silencing

(Submitter supplied) Constitutive heterochromatin in Arabidopsis thaliana is marked by repressive chromatin modifications including DNA methylation, histone 3 dimethylation at lysine 9 (H3K9me2), and monomethylation at lysine 27 (H3K27me1). The enzymes catalyzing DNA methylation and H3K9me2 have been identified and mutations in these proteins lead to the reactivation of silenced heterochromatic elements. The enzymes responsible for heterochromatic H3K27me1, in contrast, remain unknown. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL9062
2 Samples

Download data

Series

Accession:: GSE16071

ID:: 200016071

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Select item 2001118145.

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression

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

Organism:: Arabidopsis thaliana

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

Platform:: GPL17639
83 Samples

Download data: BEDGRAPH, TXT, WIG

Series

Accession:: GSE111814

ID:: 200111814

PubMed Full text in PMC Similar studies

Select item 2001118136.

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [sRNA-Seq]

(Submitter supplied) We performed Illumina sequencing of sRNA libraries prepared from 10-day-old seedlings in Arabidopsis. SE is a key component in miRNA processing and pre-mRNA splicing, whereas ATXR5/6 is engaged in epigenetic silencing. Genome-wide sRNA sequencing revealed that ATXR5/6 did not participate in SE-mediated miRNA biogenesis.

Organism:: Arabidopsis thaliana

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

Platform:: GPL17639
23 Samples

Download data: TXT

Series

Accession:: GSE111813

ID:: 200111813

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Select item 2001118127.

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [RNA-Seq]

(Submitter supplied) We performed Illumina sequencing of ribosome depletion RNA libraries prepared from 10-day-old seedlings in Arabidopsis. SE is required for transposon reactivation in atxr5 atxr6 mutant.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17639
24 Samples

Download data: TXT

Series

Accession:: GSE111812

ID:: 200111812

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001118118.

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [ChIP-Seq]

(Submitter supplied) We performed ChIP-seq of SE and selected histone modifications. ATXR5/6 deposit histone3 lysine27 monomethylation (H3K27me1) to promote heterochromatin formation and repress transposable elements (TEs) in Arabidopsis. SE binds to ATXR5/6-regulated TE loci and promotes H3K27me1 accumulation in these regions.

Organism:: Arabidopsis thaliana

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

Platform:: GPL17639
30 Samples

Download data: BEDGRAPH

Series

Accession:: GSE111811

ID:: 200111811

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001117429.

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [Bisulfite-Seq]

(Submitter supplied) We performed whole genome bisulfite sequencing in se-2 and the related triple mutants. se-2 mutant did not display obvious changes in genome wide methylation in CG, CHG and CHH contexts. Thus, the H3K27me1 hypomethylation and suppression of atxr5/6-reactivated loci in se-2 mutant was not through DNA methylation defect.

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL17639
6 Samples

Download data: WIG

Series

Accession:: GSE111742

ID:: 200111742

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Select item 20016689710.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: blank sample; Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:: GPL21785 GPL26208 GPL29487
241 Samples

Download data: BW, FPKM_TRACKING, TXT, WIG

Series

Accession:: GSE166897

ID:: 200166897

PubMed Full text in PMC Similar studies

Select item 20016689611.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_med]

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21785
8 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE166896

ID:: 200166896

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016689412.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [SMARTSeq2]

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: Arabidopsis thaliana; blank sample

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL29487 GPL26208
41 Samples

Download data: TXT

Series

Accession:: GSE166894

ID:: 200166894

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016689313.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_22]

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26208
12 Samples

Download data: WIG

Series

Accession:: GSE166893

ID:: 200166893

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016689214.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_20]

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21785
15 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE166892

ID:: 200166892

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016689115.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_17-18]

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21785
26 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE166891

ID:: 200166891

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016689016.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_16]

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21785
16 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE166890

ID:: 200166890

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016688817.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_15]

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21785
6 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE166888

ID:: 200166888

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016688718.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq-12_13]

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21785
8 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE166887

ID:: 200166887

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016688619.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_11]

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21785
24 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE166886

ID:: 200166886

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016688520.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_9_12]

(Submitter supplied) ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21785
24 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE166885

ID:: 200166885

PubMed Full text in PMC Similar studies SRA Run Selector

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