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Arabidopsis thaliana

ABSTRACT: An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [leaves RNA-seq]

PROVIDER: PRJNA155791 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR419182.fastq.gz	Fastqsanger.gz
	SRR419183.fastq.gz	Fastqsanger.gz
	SRR419184.fastq.gz	Fastqsanger.gz
	SRR419185.fastq.gz	Fastqsanger.gz
	SRR419186.fastq.gz	Fastqsanger.gz

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An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

Project description:This SuperSeries is composed of the following subset Series: GSE36129: An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [leaves RNA-seq] GSE36143: An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [BS-seq] GSE37206: An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [flowers RNA-seq] Refer to individual Series

2012-05-25 | E-GEOD-36148 | biostudies-arrayexpress

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IDN2 Interacts with RPA and Facilitates DNA Double-Strand Break Repair by Homologous Recombination in Arabidopsis

Project description:Repair of DNA double-strand break (DSB) is critical for the maintenance of genome integrity. We have previously shown that a class of DSB-induced small RNAs (diRNAs) facilitates homologous recombination (HR)-mediated DSB repair in Arabidopsis thaliana. Here we show that INVOLVED IN DE NOVO 2 (IDN2), a double-stranded RNA (dsRNA) binding protein involved in small RNA-directed DNA methylation, is required for DSB repair in Arabidopsis. We find that IDN2 interacts with the heterotrimeric replication protein A (RPA) complex. Depletion of IDN2 or the diRNA-binding ARGONAUTE 2 (AGO2) leads to increased accumulation of RPA at DSB sites and mislocalization of the recombination factor RAD51. These findings support a model in which IDN2 interacts with RPA and facilitates the release of RPA from ssDNA tails and subsequent recruitment of RAD51 at DSB sites to promote DSB repair.

2017-02-28 | GSE94305 | GEO

Noncoding RNA-mediated DNA methylation directs nucleosome positioning

Project description:We explored the mechanism by which RdDM affects nucleosome positioning in Arabidopsis thaliana. We showed that POLV has a direct effect on nucleosomes through the SWI/SNF complex. We found that the AGO4-siRNA complex is involved in nucleosome positioning via IDN2. Moreover, the SWI/SNF complex is not required for DNA methylation in positioned nucleosomes. Instead, we found that DNA methylation is needed for nucleosome positioning in differentially methylated regions. Taken together, we propose a model where the RdDM pathway directs nucleosome positioning through DNA methylation to establish transcriptional gene silencing.

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

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

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Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (RNA-Seq)

Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. Here, we report population-wide DNA sequencing of genomes, transcriptomes, and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are unlinked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified 2,372 methylQTL, which revealed the first population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically reactivated during male gametogenesis, which facilitates their silencing across generations. RNA-seq from naturally-occurring Arabidopsis accessions

2013-03-05 | E-GEOD-43858 | biostudies-arrayexpress

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