Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SWI/SNF localization during macrophage inflammatory response [ChIP-seq_SWISNF]

ABSTRACT: To understand how the SWI/SNF complex help establish appropriate epiegentic landscape during macrophage inflammatory response, we profiled the binding sites of BRG1 (all BAF), ARID1A (cBAF), BRD9 (ncBAF), and PHF10 (PBAF) for WT BMDMs with 0hr, 1hr, or 4hr LipidA stimulation. To assess the modes of action for cBAF inhibitor BRDK98, we also performed ARID1A ChIP for BRDK98-treated BDMDs after 0hr and 4hr of LipidA stimulation.

ORGANISM(S): Mus musculus

PROVIDER: GSE242801 | GEO | 2024/06/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effect of SWI/SNF pertubations on chromatin accessibility during macrophage inflammatory activation [ATAC-seq]

Project description:To understand how macrophage chromatin respond to LipidA stimulation, we profiled accessibility for WT BMDMs with 0hr, 1hr, or 4hr LipidA stimulation. In addition, we also profiled accessibility for WT BMDMs treated with ACBI1, BRM014, BRDK98, or dBrd9 and for Arid1A-/- Pbrm1-/- BMDMs after 0hr, 1hr, or 4hr LipidA stimulation.

2024-06-05 | GSE242799 | GEO

Effect of SWI/SNF pertubations on macrophage inflammatory activation [RNA-seq]

Project description:To characterize macrophage inflammtory activation and the role of the SWI/SNF complex, we first profiled gene expression for WT BMDMs with 0hr, 1hr, or 4hr LipidA stimulation. In addition, we also profiled gene expression for WT BMDMs treated with ACBI1, BRM014, or BRDK98 treatment and for Arid1A-/- or Pbrm1-/- BMDMs after 1hr or 4hr LipidA or LPS stimulation.

2024-06-05 | GSE242802 | GEO

Effect of SWI/SNF pertubations on H3K27ac levels during macrophage inflammatory activation [ChIP-seq_Histone]

Project description:To understand how macrophage histone modifications respond to LipidA stimulation, we profiled H3K27ac binding for WT BMDMs with 0hr or 4hr LipidA stimulation. In addition, we also profiled H3k27ac levels for WT BMDMs treated with ACBI1, BRM014, BRDK98, or dBrd9 and for Arid1A-/- and Pbrm1-/- BMDMs after 4hr LipidA stimulation.

2024-06-05 | GSE242800 | GEO

Genome-wide maps of SWI/SNF complexes binding in WT and ARID1-less H2.35 cells

Project description:Globally, the three categories of intact SWI/SNF complexes in control cells have shared and unique binding peaks, with cBAF showing the most abundant binding sites followed by ncBAF and pBAF. In control cells, within cBAF, ARID1B bound to only a subset of ARID1A peaks. In control cells, the binding pattern of BAF45d corresponded to ARID1A patterns, but binding was virtually eliminated in ARID1-less cells. In ARID1-less cells, ARID2 binding was essentially eliminated whereas Brd9 binding was unaltered.

2020-06-10 | GSE140183 | GEO

A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation

Project description:Mammalian SWI/SNF chromatin remodeling complexes exist in three distinct, final-form assemblies: canonical BAF (cBAF), PBAF, and a newly characterized non-canonical complex, ncBAF. However, their complex-specific targeting on chromatin, functions and roles in disease remain largely unknown. Here, we comprehensively map complex assemblies on chromatin and find that ncBAF uniquely localizes to CTCF sites and promoters. We identified ncBAF subunits as major synthetic lethalities specific to human synovial sarcoma and malignant rhabdoid tumor, which share in common cBAF complex perturbation. Chemical and biological depletion of the BRD9 subunit of ncBAF rapidly attenuates SS and MRT cell proliferation. Notably, in cBAF-perturbed cancers, ncBAF complexes retain localization to CTCF sites and promoters, and maintain gene expression at retained mSWI/SNF sites to support cell proliferation in a manner distinct from fusion oncoprotein-mediated targeting. Taken together, these findings unmask the unique targeting and function of ncBAF complexes and present new cancer-specific therapeutic targets.

2018-11-06 | PXD011103 | Pride

BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state [human_Brd9_CTCF-ChIP-seq]

Project description:Switch/sucrose nonfermentable (SWI/SNF) complexes are ATP-dependent chromatin remodeler complexes that play critical roles in timely and appropriate gene regulation by modulating chromatin architecture and DNA accessibility. SWI/SNF complexes can be grouped into three subcomplexes of differing sizes, canonical BAF (cBAF), polybromo BAF (PBAF), and newly identified noncanonical BAF (ncBAF). The most recently characterized ncBAF lacks the core BAF subunits ARID, BAF47, and BAF57, but includes unique subunits GLTSCR1/1L and BRD9, one of the bromodomain-containing proteins.We recently demonstrated the novel mechanism for the ncBAF disruption caused by mutations in a spiceosomal protein, SF3B1, especially in 65–83% for myelodysplastic syndromes (MDS) with ring sideroblasts as well as in >20% of mucosal/uveal melanomas, suggesting that the disturbed ncBAF may have some roles in the malignant hematopoiesis.Mechanistically, SF3B1 mutant recognizes an aberrant, deep intronic branchpoint within BRD9 and thereby induces the inclusion of an aberrant exon and subsequently profound degradation of BRD9 mRNA by triggering nonsense-mediated RNA decay (NMD). However, compared to the roles of cBAF, the functions of BRD9/ncBAF in normal and malignant hematopoiesis in vivo have been totally uncharacterized.

2023-10-31 | GSE236328 | GEO

BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state [human_Brd9_bulkRNA-seq]

2023-10-31 | GSE236327 | GEO

BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state [human_Brd9_ATAC-seq]

2023-10-31 | GSE236326 | GEO

BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state [Mouse_Brd9_CTCF ChIP-seq]

2023-11-01 | GSE236959 | GEO

BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state [MOLM13 DMSO vs dBRD9 RNA-seq]

2023-11-01 | GSE236958 | GEO