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Target genes of BRG1 in human embryonic stem cells

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57473 | GEO | 2015/04/28

SECONDARY ACCESSION(S): PRJNA246524

REPOSITORIES: GEO

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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

Target genes of BRG1 in mouse embryonic stem cells

2015-04-28 | GSE57472 | 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

Comparison of BRG1 reexpression, TSA treatment and 5dAzaC treatment on gene expression in human NCI-H522 NSCLC cells

Project description:Transcription was assessed in the human H522 NSCLC cell line after reexpression of BRG1, one of the mutually exclusive subunits of the SWI/SNF chromatin remodeling complex, by adenovirus infection, after treatment with 5 micromolar 5-deAzacytidine or after treatment with 100nM Trichostatin A. Control treatments included infection with adenovirus expressing GFP and treatment with DMSO4 (vehicle control). The goal of the experiment was to identify target genes of the SWI/SNF complex and compart them to changes induced by DNA methylation and histone acetylation modifiers. One biological replicate of each treatment; 4 technical replicates of each treatment.

2014-01-13 | E-GEOD-54033 | biostudies-arrayexpress

Signal-dependent incorporation of MyoD-BAF60c into Brg1-based SWI/SNF chromatin-remodeling complex

Project description:Tissue-specific transcription factors initiate differentiation toward a specialized cell type by inducing transcription-permissive chromatin modifications at target gene promoters, through the recruitment of the SWI/SNF chromatin-remodeling complex (1, 2). The molecular mechanism that regulates the chromatin re-distribution of SWI/SNF in response to differentiation signals is currently unknown. Here we show that the muscle determination factor MyoD and the SWI/SNF structural sub-unit, BAF60c (SMARCD3), form a complex on the regulatory elements of MyoD-target genes in undifferentiated myoblasts, prior to the activation of gene expression. MyoD-BAF60c complex is devoid of the ATP-dependent enzymatic sub-units Brg1 and Brm, is required for stable MyoD binding to Ebox sequences, and marks the chromatin for signal-dependent recruitment of the SWI/SNF core complex to muscle loci. BAF60c phosphorylation on a conserved threonine by differentiation-activated p38 signalling promotes the incorporation of MyoD-BAF60c into a Brg1-based SWI/SNF complex, which is competent to remodel the chromatin and activates transcription of MyoD-target genes. Our data support an unprecedented two-step model, by which pre-assembled BAF60c-MyoD complex directs the SWI/SNF complex chromatin re-distribution to muscle loci in response to differentiation cues. Differentiation of C2C12 cells individually interfered for BRG1, BAF60B, BAF60C

2011-03-07 | E-GEOD-24573 | biostudies-arrayexpress

Comparison of gene expression in control and BRG1-knockdown H358 cell lines

Project description:Transcription was assessed in the human H358 NSCLC cell line after knockdown of BRG1, one of the mutually exclusive subunits of the SWI/SNF chromatin remodeling complex, by 2 different shRNAs. One biolgical replicate of each treatment; 4 technical replicates of each treatment.

2014-09-23 | E-GEOD-58542 | biostudies-arrayexpress

Comparison of BRG1 reexpression, TSA treatment and 5dAzaC treatment on gene expression in human NCI-H522 NSCLC cells

2014-01-13 | GSE54033 | GEO

Brd7, a novel PBAF-specific SWI/SNF subunit, is required for gene activation and repression in embryonic stem cells

Project description:The composition of chromatin remodeling complexes dictates how these enzymes control transcriptional programs and cellular identity. Here, we investigate the composition of SWI/SNF complexes in embryonic stem cells (ESCs). In contrast to differentiated cells, ESCs have a biased incorporation of certain paralogous SWI/SNF subunits, with low levels of Brm, BAF170 and ARID1B. Upon differentiation, the expression of these subunits increases, resulting in a higher diversity of compositionally distinct SWI/SNF enzymes. We also identify Brd7 as a novel component of the PBAF complex in both ESCs and differentiated cells. Using shRNA-mediated depletion of Brg1, we show that SWI/SNF can function as both a repressor and an activator in pluripotent cells, regulating expression of developmental modifiers and signaling components such as Nodal, ADAMTS1, Bmi-1, CRABP1 and TRH. Knock-down studies of PBAF-specific Brd7 and of a signature subunit within the BAF complex, ARID1A, show that these two sub-complexes affect SWI/SNF target genes differentially, in some cases even antagonistically. This may be due to their different biochemical properties. Finally, we examine the role of SWI/SNF in regulating its target genes during differentiation. We find that SWI/SNF affects recruitment of components of the pre-initiation complex in a promoter-specific manner, to modulate transcription positively or negatively. Taken together, our results provide insight into the function of compositionally diverse SWI/SNF enzymes that underlie their inherent gene-specific mode of action. R1 ESCs were infected in duplicates with shRNA targeting Brg1 or GLUT4 (as a control). Knockdown of Brg1 mRNA affected Brg1 protein levels efficiently. RNA was isolated 67 hours post-infection and analyzed using microarrays.

2010-03-04 | E-GEOD-7791 | biostudies-arrayexpress

The B-cell CLL/lymphoma 7 (BCL7) protein family members drive gene expression changes via interactions with the Brahma Related Gene 1 (BRG1) Helicase-Sant Associated domain (HSA) domain [LongTerm]

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. We identified a family of SWI/SNF complex members, the BCL7 proteins, as critical components to drive BRG1-dependent gene expression changes. The BCL7 proteins have been implicated in B-cell lymphoma, but the characterization of their functional role within the SWI/SNF complex has not been fully explored. This study implicates their critical function alongside BRG1 to cause large scale changes in gene expression. Mechanistically, the BCL7 proteins bind to the HSA domain of BRG1 and require this domain for stable protein expression and binding to chromatin. These results provide a link between the HSA domain and the formation of a stable functional SWI/SNF remodeling complex through the interaction with the BCL7 proteins. The data shown here highlights the importance of proper formation of the SWI/SNF complex to drive critical biological functions, as losses of members that were once considered minor accessory components can cause severe loss of complex function.

2022-11-17 | GSE188727 | GEO

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