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A bifunctional nucleosome binding protein mediates specialized mSWI/SNF complex targeting and activity

ABSTRACT: A bifunctional nucleosome binding protein mediates specialized mSWI/SNF complex targeting and activity

PROVIDER: PRJNA578154 | ENA |

REPOSITORIES: ENA

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A bifunctional nucleosome binding protein mediates specialized mSWI/SNF complex targeting and activity (RNA-seq dataset)

Project description:Here we identify and characterize a minimal domain within the SS18-SSX fusion oncoprotein hallmark to synovial sarcoma, that exhibits a high-affinity interaction with the nucleosome acidic patch. We find that this region is necessary and sufficient for nucleosome binding, mSWI/SNF (BAF) chromatin remodeling complex targeting, catalytic activity, and activation of cancer-specific gene expression. Moreover, we identify PRC1-mediated H2AUb119 as a further rheostat governing further stability and binding. Together, our results define an unexpected direct bifunctional histone detector on SSX that is responsible for disease-specific chromatin recruitment of a major family of chromatin regulatory complexes.

2020-08-04 | GSE139054 | GEO

A bifunctional nucleosome binding protein mediates specialized mSWI/SNF complex targeting and activity (ChIP-seq dataset)

2020-08-04 | GSE139053 | GEO

A bifunctional nucleosome binding protein mediates specialized mSWI/SNF complex targeting and activity (ChIP-seq dataset)

Project description:A bifunctional nucleosome binding protein mediates specialized mSWI/SNF complex targeting and activity (ChIP-seq dataset)

| PRJNA578157 | ENA

A bifunctional nucleosome binding protein mediates specialized mSWI/SNF complex targeting and activity (RNA-seq dataset)

Project description:A bifunctional nucleosome binding protein mediates specialized mSWI/SNF complex targeting and activity (RNA-seq dataset)

| PRJNA578158 | ENA

A bifunctional nucleosome binding protein mediates specialized mSWI/SNF complex targeting and activity

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

2020-08-04 | GSE139055 | GEO

The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [ChIP-seq]

Project description:Perturbations to mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complexes have been widely implicated as driving events across cancers1. One such perturbation is the dual loss of the SMARCA4 and SMARCA2 ATPase subunits, which has recently been implicated in rare cancers such as small cell carcinoma of the ovary, hypercalcemic type (SCCOHT)2-5, SMARCA4-deficient thoracic sarcomas6 and dedifferentiated endometrial carcinomas7. The consequences of SMARCA4/2 dual loss on the biochemical composition of the complex, chromatin targeting and remodeling capabilities, and subcomplex identity (BAF vs. PBAF) in these cancers are unknown. Here, we leverage SCCOHT cell lines to identify an unexpected ATPase module of mSWI/SNF subunits. Using biochemical and genome-wide profiling assays, we found that the incorporation of the ATPase module is a critical step in the functional specification of BAF and PBAF subcomplexes. Furthermore, by utilizing ATPase mutant variants, we found that the ATPase module mediates two separate and concurrent mSWI/SNF targeting mechanisms, evenly split between catalytically-independent targeting to primed enhancers/promoters and catalytically-dependent targeting to de novo enhancers. Finally, by linking these distinct sites to separate tumor-suppressive gene expression programs across ovarian tissues , we clarify the mechanistic consequences of SMARCA4/2 loss dual loss in these rare tumors.

2019-03-11 | GSE117734 | GEO

The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [RNA-seq]

2019-03-11 | GSE117311 | GEO

The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [ATAC-seq]

2019-03-11 | GSE117301 | GEO

Identifying the genomic regions co-bound by ASCL1 and mSWI/SNF remodelers during neural differentiation [ChIP-seq]

Project description:We interfeered with the ASCL1-mSWI/SNF interaction: to abolish ASCL1 function, we knocked out ASCL1 in human iPSCs, while we used the BRM014 inhibitor to block the mSWI/SNF ATPase activity. We then performed ASCL1 ChIPseq in DIV24 WT and BRM014-treated neural cultures, and SMARCB1 ChIPseq in DIV24 WT and ASCL1 KO neural cultures, when ASCL1 expression is highest.

2023-03-14 | GSE214381 | GEO

mSWI/SNF functional genomic characterization of SMARCB1 mutants in SMARCB1-null and heterozygous settings

Project description:Chromatin remodeling complexes regulate gene expression by shifting, evicting, and exchanging nucleosomes along the chromosomes of eukaryotic organisms. The mammalian SWI/SNF chromatin remodeling complex (mSWI/SNF or BAF) is mutated in over 20% of human cancers and loss of the SMARCB1 gene, encoding the BAF47 protein subunit, results in one of the most aggressive and lethal pediatric cancers. An accumulation of point mutations occurs at the C-terminal end of the protein, for which the functional ramifications are unknown. We previously demonstrated that reintroduction of SMARCB1 in SMARCB1-null malignant rhabdoid tumor cells results in a genome-wide increase of mSWI/SNF complex occupancy coupled with activation of PRC2-repressed genes. Here, we study the functional consequences that these point mutations exert on mSWI/SNF complex activity in SMARCB1-deficient tumor cells and extend this investigation to a CRISPR/Cas9-mediated SMARCB1-heterozygous mutant induced pluripotent stem cell. Intriguingly, we observe that the mutant complexes bind similarly to wild-type SMARCB1 complexes at enhancers throughout the genome but often fail to transcriptionally activate nearby genes in a cis-regulatory manner.

2019-11-21 | GSE124903 | GEO

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