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Four SWI2/SNF2 chromatin remodeling proteins play roles as “double agents” in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis [Bisulfite-seq]

ABSTRACT: Four SWI2/SNF2 chromatin remodeling proteins play roles as “double agents” in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis [Bisulfite-seq]

PROVIDER: PRJNA433497 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6687450_1.fastq.gz	Fastqsanger.gz
	SRR6687450_2.fastq.gz	Fastqsanger.gz
	SRR6687460_1.fastq.gz	Fastqsanger.gz
	SRR6687460_2.fastq.gz	Fastqsanger.gz
	SRR6687451_1.fastq.gz	Fastqsanger.gz

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Four SWI2/SNF2 chromatin remodeling proteins play roles as “double agents” in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis [small RNA]

Project description:Here we report that CLSY4 and its three paralogous SWI2/SNF2-type chromatin remodeling proteins function in both RdDM and active DNA demethylation for dynamic regulation of DNA methylation in Arabidopsis. We identified CLSY4 initially in a genetic screen for DNA demethylation factors and subsequently demonstrated that it also plays an important role in RdDM. Comprehensive genetic analyses using single and high order mutants of CLSY family proteins revealed their roles as double agents in the tug of war between methylation and demethylation reactions. The four CLSY proteins collectively are necessary for the canonical RdDM pathway; meanwhile, each CLSY also mediates active DNA demethylation at specific loci where DNA methylation is dependent on one or more of the other three CLSY proteins. Our results revealed dual functions of the four chromatin remodeling proteins in regulating genomic DNA methylation status, and thus provide new insights into the mechanisms underlying the dynamic regulation of DNA methylation in Arabidopsis.

2018-10-29 | GSE110337 | GEO

Four SWI2/SNF2 chromatin remodeling proteins play roles as “double agents” in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis [Bisulfite-seq]

2018-10-29 | GSE110336 | 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

Four SWI2/SNF2 chromatin remodeling proteins play roles as "double agents" in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis

Project description:Four SWI2/SNF2 chromatin remodeling proteins play roles as "double agents" in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis

| PRJNA433491 | ENA

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

Four SWI2/SNF2 chromatin remodeling proteins play roles as “double agents” in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis [small RNA]

Project description:Four SWI2/SNF2 chromatin remodeling proteins play roles as “double agents” in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis [small RNA]

| PRJNA433498 | ENA

Four SWI2/SNF2 chromatin remodeling proteins play roles as "double agents" in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis

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

2018-10-29 | GSE110338 | GEO

Panicum virgatum strain:WAR | cultivar:WAR

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Project description:Mot1 is a conserved Snf2/Swi2-related transcriptional regulator that uses ATP hydrolysis to displace TATA-binding protein (TBP) from DNA. Several models of the enzymatic mechanism have been proposed, including Mot1-catalyzed distortion of TBP structure, competition between Mot1 and DNA for the TBP DNA-binding surface, and ATP-driven translocation of Mot1 along DNA. Here, DNase I footprinting studies provide strong support for a 'DNA-based' mechanism of Mot1, which we propose involves ATP-driven DNA translocation. Mot1 forms an asymmetric complex with the TBP core domain (TBPc)-DNA complex, contacting DNA both upstream and within the major groove of the TATA Box. Contact with upstream DNA is required for Mot1-mediated displacement of TBPc from DNA. Using the SsoRad54-DNA complex as a model, DNA-binding residues in Mot1 were identified that are critical for Mot1-TBPc-DNA complex formation and catalytic activity, thus placing Mot1 mechanistically within the helicase superfamily. We also report a novel ATP-independent TBPc displacement activity for Mot1 and describe conformational heterogeneity in the Mot1 ATPase, which is likely a general feature of other enzymes in this class.

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Transcriptome of the Wistar audiogenic rat (WAR) strain following audiogenic seizures

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2020-06-13 | GSE152339 | GEO

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