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Genome-wide maps of BRG1 binding sites in cortical neuron under basal and depolarized conditions [ChIP-seq]

ABSTRACT: CHIP-seq analysis of BRG1 binding sites in cultured cortical neurons revealed a depolarization induced BRG1 binding to neuronal inducible enahncers.

ORGANISM(S): Mus musculus

PROVIDER: GSE174581 | GEO | 2021/05/18

REPOSITORIES: GEO

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Genome-wide maps of BRG1 binding sites in cortical neuron under basal and depolarized conditions [ChIP-seq]

Project description:Genome-wide maps of BRG1 binding sites in cortical neuron under basal and depolarized conditions [ChIP-seq]

| PRJNA730573 | ENA

Open chromatin sites identified in wildtype and Brg1-cko neurons in basal and depolarized conditions [ATAC-seq]

Project description:ATAC-seq analyses examined open chromatin regions in of wildtype and Brg1-cko neurons in basal and depolarized conditions.

2021-05-18 | GSE174579 | GEO

Protein-protein interactions of BRG1 or BRG1-HSA in SW13 cells

Project description:The SWI/SNF complex remodels chromatin in an ATP-dependent manner through the ATPase subunits BRG1 and BRM. Chromatin remodeling alters nucleosome structure to change gene expression, however aberrant remodeling and gene expression can result in cancer. The function and localization on chromatin of the SWI/SNF complex depends on the protein makeup of the complex. Here we report the protein-protein interactions of wild-type BRG1 or mutant BRG1 in which the HSA domain has been deleted (BRG1-HSA). We demonstrate the interaction of BRG1 with most SWI/SNF complex members and a failure of a number of these members to interact with BRG1-HSA. These results demonstrate that the HSA domain of BRG1 is a critical interaction platform for the correct formation of SWI/SNF remodeling complexes.

2023-02-15 | PXD029647 | Pride

Dynamic BRG1 Recruitment During T Helper Differentiation And Activation Reveals Distal Regulatory Elements

Project description:We found binding of the remodeling protein BRG1 was programmed by lineage and activation signals. BRG1 binding was positively correlated with gene activity at protein-coding and miRNA genes. BRG1 binding was found at promoters and distal regions, including known and novel distal regulatory elements. Distal BRG1 binding correlated with expression, and novel distal sites possessed enhancer activity, suggesting a general role for BRG1 in long-distance gene regulation. Together, these findings suggest BRG1 interprets differentiation and activation signals and plays a causal role in gene regulation, chromatin structure, and cell fate. Our findings indicate BRG1 binding is a useful marker for identifying cis-regulatory regions in protein-coding and miRNA genes. Compare BRG1 binding in T helper subsets genome wide; Naïve, resting Th1, resting Th2, Stimulated Th1, Stimulated Th2, Stimulated Th17, compared to input DNA as negative control

2011-03-01 | E-GEOD-23719 | biostudies-arrayexpress

Target genes of BRG1 in mouse embryonic stem cells

Project description:BRG1-SWI/SNF complex is an important chromatin remodeling complex that involved in various biological processes. Here we described the genome-wide binding of histone acetylation upon BRG1 depletion in mouse embryonic stem cells. Mouse embryonic stem cells were treated with either scrambled siRNA or siRNA against BRG1 for 48 h, and each treatment has three replicates.

2015-04-28 | E-GEOD-57472 | biostudies-arrayexpress

Target genes of BRG1 in human embryonic stem cells

Project description:BRG1-SWI/SNF complex is an important chromatin remodeling complex that involved in various biological processes. Here we described the genome-wide binding of histone acetylation upon BRG1 depletion in human embryonic stem cells. Human embryonic stem cells were treated with either scrambled siRNA or siRNA against BRG1 for 48 h, and each treatment has three replicates.

2015-04-28 | E-GEOD-57473 | biostudies-arrayexpress

CircRNA analysis in depolarized neuroblastoma cells

Project description:We profiled circRNA using RNA-seq in the depolarized neuroblastoma cells to detect depolarization associated circRNAs

2020-03-06 | GSE139010 | GEO

Regulation of nucleosome landscape and transcription factor binding at enhancers by BRG1

Project description:Enhancers of transcription activate transcription via binding of sequence-specific transcription factors to their target sites in chromatin. In this report, we identify GATA1-bound enhancers genome-wide and find a global reorganization of the nucleosomes at these enhancers during differentiation of hematopoietic stem cells (HSCs) to erythrocytes. We show that the catalytic subunit BRG1 of BAF complexes localizes to these enhancers during differentiation and generates a longer nucleosome repeat length surrounding the GATA1 sites by shifting the flanking nucleosomes away. Intriguing, we find that the nucleosome shifting specifically facilitates binding of TAL1 but not GATA1, which subsequently activates transcription of target genes. Human hematopoietic stem cells (referred as CD34+ cells) were differentiated into erythroid lineage expressing the cell surface marker CD36 (referred as CD36+ cells). To study the function of ATP-dependent chromatin remodeling BAF complexes in the establishment of erythroid specific enhancers during differentiation, we mapped the genome-wide binding sites of GATA1 and TAL1, the key transcription regulators of erythroid differentiation, in CD36+ cells, then determined the genomic positions of the catalytic subunit BRG1 of the BAF complexes and the nucleosome landscapes, by ChIP-Seq and Mnase-Seq, respectively, for both HSCs and the differentiated cells. We compared changes in nucleosome landscapes with BRG1 binding at GATA1 and TAL1 binding sites and found that BRG1 binding is correlated with nucleosome shifting away from the binding sites, which is critical for TAL1 binding. To confirm that BRG1 is responsible for the nucleosome shift, we knocked down BRG1 in CD36+ cells and analyzed the nucleosome changes in the knockdown cells. The data indicated that inhibition of BRG1 caused a nucleosome shift towards the GATA1 or TAL1 sites, indicating that BRG1 is indeed responsible for the observed nucleosome shift.

2011-07-01 | E-GEOD-26501 | biostudies-arrayexpress

ChIP-seq analysis of genome wide Brg1 binding in mouse primary keratinocytes

Project description:We analyzed Brg1 binding genomeiwide in freshly isolated newborn mouse epidermal keratinocytes using ChIP-seq technology Mouse epidermal keratinocytes were isolated form the newborn C57Bl6 mice and Brg1 binding in their chromatin was analyzed using ChIP-seq technology on Hi-Seq 2500 machine

2013-11-01 | E-GEOD-50921 | biostudies-arrayexpress

Dynamic BRG1 Recruitment During T Helper Differentiation And Activation Reveals Distal Regulatory Elements

2011-03-01 | GSE23719 | GEO

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