Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA433491 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			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

Items per page:

1 - 5 of 38

Similar Datasets

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

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 [Bisulfite-seq]

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 [Bisulfite-seq]

| PRJNA433497 | 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 [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

Project description:Panicum virgatum WAR Resequencing genome sequencing

| PRJNA334774 | ENA

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.

| S-EPMC1440317 | biostudies-literature

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

Project description:The Wistar Audiogenic Rat (WAR) is a model whose rats are predisposed to develop seizures following acoustic stimulation. We aimed to establish the transcriptional profile of the WAR model, searching for genes that help in understanding the molecular mechanisms involved in the predisposition and seizures expression of this strain. RNA-Seq of the corpora quadrigemina of WAR and Wistar rats subjected to acoustic stimulation revealed 64 genes differentially regulated in WAR. We validated twelve of these genes by qPCR in stimulated and naive (nonstimulated) WAR and Wistar rats. Among these, Acsm3 was upregulated in WAR in comparison with both control groups. In contrast, Gpr126 and Rtel1 were downregulated in naive and stimulated WAR rats in comparison with the Wistar controls. Qdpr was upregulated only in stimulated WAR rats that exhibited audiogenic seizures. Our data show that there are genes with differential intrinsic regulation in the WAR model and that seizures can alter gene regulation. We identified new genes that might be involved in the epileptic phenotype and comorbidities of the WAR model.

2020-06-13 | GSE152339 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data