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An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [BS-seq]

ABSTRACT: Illumina-based whole genome bisulfite sequencing libraries for 4 RNA-directed DNA methylation mutants

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE36143 | GEO | 2012/05/26

SECONDARY ACCESSION(S): PRJNA155799

REPOSITORIES: GEO

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An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [BS-seq]

Project description:Illumina-based whole genome bisulfite sequencing libraries for 4 RNA-directed DNA methylation mutants Examining DNA methylation levels in leaf tissue of RNA-directed DNA methylation mutants

2012-05-26 | E-GEOD-36143 | biostudies-arrayexpress

An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis (flowers RNA-seq)

Project description:Illumina mRNA libraries for 7 RNA-directed DNA methylation mutants.

2012-05-26 | GSE37206 | GEO

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

Project description:Illumina TruSeq mRNA libraries for 4 RNA-directed DNA methylation mutants

2012-05-26 | GSE36129 | GEO

An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis (flowers RNA-seq)

Project description:Illumina mRNA libraries for 7 RNA-directed DNA methylation mutants. Examining mRNA levels in floral tissue of RNA-directed DNA methylation mutants.

2012-05-26 | E-GEOD-37206 | biostudies-arrayexpress

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

Project description:Illumina TruSeq mRNA libraries for 4 RNA-directed DNA methylation mutants Examining mRNA levels in leaf tissue of RNA-directed DNA methylation mutants

2012-05-26 | E-GEOD-36129 | biostudies-arrayexpress

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

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2012-05-26 | GSE36148 | GEO

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

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

| PRJNA152967 | ENA

INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.

Project description:At least three pathways control maintenance of DNA cytosine methylation in Arabidopsis thaliana. However, the RNA-directed DNA methylation (RdDM) pathway is solely responsible for establishment of this silencing mark. We previously described INVOLVED IN DE NOVO 2 (IDN2) as being an RNA-binding RdDM component that is required for DNA methylation establishment. In this study, we describe the discovery of two partially redundant proteins that are paralogous to IDN2 and that form a stable complex with IDN2 in vivo. Null mutations in both genes, termed IDN2-LIKE 1 and IDN2-LIKE 2 (IDNL1 and IDNL2), result in a phenotype that mirrors, but does not further enhance, the idn2 mutant phenotype. Genetic analysis suggests that this complex acts in a step in the downstream portion of the RdDM pathway. We also have performed structural analysis showing that the IDN2 XS domain adopts an RNA recognition motif (RRM) fold. Finally, genome-wide DNA methylation and expression analysis confirms the placement of the IDN proteins in an RdDM pathway that affects DNA methylation and transcriptional control at many sites in the genome. Results from this study identify and describe two unique components of the RdDM machinery, adding to our understanding of DNA methylation control in the Arabidopsis genome.

| S-EPMC3365198 | biostudies-literature

IDN2 and its paralogs form a complex required for RNA-directed DNA methylation.

Project description:IDN2/RDM12 has been previously identified as a component of the RNA-directed DNA methylation (RdDM) machinery in Arabidopsis thaliana, but how it functions in RdDM remains unknown. By affinity purification of IDN2, we co-purified two IDN2 paralogs IDP1 and IDP2 (IDN2 PARALOG 1 and 2). The coiled-coil domain between the XS and XH domains of IDN2 is essential for IDN2 homodimerization, whereas the IDN2 C-terminal XH domain but not the coiled-coil domain is required for IDN2 interaction with IDP1 and IDP2. By introducing the wild-type IDN2 sequence and its mutated derivatives into the idn2 mutant for complementation testing, we demonstrated that the previously uncharacterized IDN2 XH domain is required for the IDN2-IDP1/IDP2 complex formation as well as for IDN2 function. IDP1 is required for de novo DNA methylation, siRNA accumulation, and transcriptional gene silencing, whereas IDP2 has partially overlapping roles with IDP1. Unlike IDN2, IDP1 and IDP2 are incapable of binding double-stranded RNA, suggesting that the roles of IDP1 and IDP2 are different from those of IDN2 in the IDN2-IDP1/IDP2 complex and that IDP1 and IDP2 are essential for the functioning of the complex in RdDM.

| S-EPMC3342958 | biostudies-literature

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