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The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis

ABSTRACT: The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis

OTHER RELATED OMICS DATASETS IN: E-GEOD-62799

PROVIDER: PRJNA265182 | ENA |

REPOSITORIES: ENA

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The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis [mRNA-Seq]

Project description:DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: MET1, CMT3, DRM2, and CMT2. However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families and have partially redundant functions, such as DICER-LIKE 2, 3 and 4, and IDN2- LIKE 1 and 2. Traditional mutagenesis screens usually fail to detect genes if they are redundant, since the loss of one gene can be compensated by a related gene. In an effort to circumvent this issue, we utilized co-expression data to identify closely related genes that are co-regulated with genes in the RdDM pathway. Here we report the discovery of two redundant proteins, SNF2-RING-HELICASE-LIKE1 and 2 (FRG1 and 2) that are putative chromatin-related paralogous proteins. Analysis of genome–wide bisulfite sequencing shows that simultaneous mutations of FRG1 and 2 cause broad defects in methylation at RdDM targeted loci. We also show that FRG1 stably associates with Su(var)3-9-related SUVR2, a known RdDM component, in vivo. Combined, our results identify FRG1 and FRG2 as novel components of the RdDM machinery. mRNA profiles of 14 days old seedlings of Columbia 0 wild type and frg1-1 frg2-1 double mutants, 3 biological replicates each.

2014-11-25 | E-GEOD-62799 | biostudies-arrayexpress

The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis [small RNA-Seq]

Project description:DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: MET1, CMT3, DRM2, and CMT2. However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families and have partially redundant functions, such as DICER-LIKE 2, 3 and 4, and IDN2- LIKE 1 and 2. Traditional mutagenesis screens usually fail to detect genes if they are redundant, since the loss of one gene can be compensated by a related gene. In an effort to circumvent this issue, we utilized co-expression data to identify closely related genes that are co-regulated with genes in the RdDM pathway. Here we report the discovery of two redundant proteins, SNF2-RING-HELICASE-LIKE1 and 2 (FRG1 and 2) that are putative chromatin-related paralogous proteins. Analysis of genomeM-bM-^@M-^Swide bisulfite sequencing shows that simultaneous mutations of FRG1 and 2 cause broad defects in methylation at RdDM targeted loci. We also show that FRG1 stably associates with Su(var)3-9-related SUVR2, a known RdDM component, in vivo. Combined, our results identify FRG1 and FRG2 as novel components of the RdDM machinery. Small RNA profiles of Columbia 0 wild type, frg1-1 frg2-1 double, frg1 to 5 quintuple, suvr2-1, dcl3-1 and drm1-1 drm2-2 double mutants, 3 biological replicates each.

2014-11-25 | E-GEOD-62800 | biostudies-arrayexpress

The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis [mRNA-Seq]

2014-11-25 | GSE62799 | GEO

The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis [small RNA-Seq]

2014-11-25 | GSE62800 | GEO

A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling

Project description:The in vivo role of a novel domain in Swi2/Snf2 required for its function was investigated using microarray analysis. The effect of domain deletions of Swi2/Snf2 on expression changes were studied. The ?SnAC strain, along with ?snf2 and wild type strains (BY4741 and Snf2-2FLAG, PSY2), were analyzed by genome-wide expression profiling with DNA microarrays. The method has been described in Chitikila et al., Mol. Cell, 10:871-882, 2002 (PMID 12419230).

2011-09-14 | E-GEOD-30675 | biostudies-arrayexpress

A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling

Project description:The in vivo role of a novel domain in Swi2/Snf2 required for its function was investigated using microarray analysis.

2011-09-15 | GSE30675 | GEO

Arabidopsis thaliana

Project description:The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis [mRNA-Seq]

| PRJNA265183 | ENA

The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-11-25 | E-GEOD-62801 | biostudies-arrayexpress

The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis

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

2014-11-25 | GSE62801 | GEO

Arabidopsis thaliana

Project description:The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis [small RNA-Seq]

| PRJNA265184 | ENA

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