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Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis [ATAC-Seq]

ABSTRACT: We performed ATAC-seq on WT, BAF60c KO, and BAF170 KO CPs and CMs in 2-5 biological replicates follwing Corces et al., 2017 paper.

OTHER RELATED OMICS DATASETS IN: PXD012721

ORGANISM(S): Mus musculus

PROVIDER: GSE116295 | GEO | 2019/02/28

REPOSITORIES: GEO

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Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis

Project description:Chromatin remodeling complexes instruct cellular differentiation and lineage specific transcription. The BRG1/BRM associated factor (BAF) complexes are important for several aspects of differentiation. We show that the catalytic subunit Brg1 has a specific role in cardiac precursors (CPs) to initiate cardiac gene expression programs and repress non-cardiac expression. Using immunoprecipitation immunopurification with mass spectrometry we determined the dynamic composition of BAF complexes during mammalian cardiac differentiation, identifying several cell-type specific subunits. We focused on the CP- and cardiomyocytes (CM)-enriched subunits BAF60c (SMARCD3) and BAF170 (SMARCC2). Baf60c and Baf170 co-regulate gene expression with Brg1 in CPs, and in CMs their loss results in broadly deregulated cardiac gene expression. BRG1, BAF60, and BAF170 modulate chromatin accessibility, to either promote accessibility at activated genes, while closing up chromatin at repressed genes. BAF60c and BAF170 are required for proper BAF complex composition, and BAF170 loss leads to retention of BRG1 at CP-specific enhancers. Thus, dynamic interdependent BAF complex subunit assembly modulates chromatin states and thereby participates in directing temporal gene expression programs in cardiogenesis.

2019-11-13 | PXD012721 | Pride

Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis [RNA-Seq III]

Project description:We compared differential gene expression between WT and BAF60c KO and between WT and BAF170 KO cardiac precursors and cardiomyocytes

2019-02-28 | GSE116279 | GEO

Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis [ChIP-Seq]

Project description:Genome-wide occupancy analysis of BRG1 during cardiac precursor and crdiomyocyte stages of differentiation in WT and cells lacking BAF60c or BAF170

2019-02-28 | GSE116281 | GEO

ATACseq of WT and BRM KO cells at D4, D6 and D10 of cardiac differentiation

Project description:We performed ATAC-seq on WT, BAF60c KO, BAF170 KO and BRM KO CPs and CMs in 2-5 biological replicates follwing Corces et al., 2017 paper. Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization How robust canalization is established or maintained is unclear. Here we show that deletion of the BRG1/BRM-associated factor (BAF) chromatin remodeling complex ATPase gene Brm (encoding Brahma) results in a radical identity switch during directed cardiogenesis of mouse embryonic stem cells (ESCs). Despite establishment of well-differentiated precardiac mesoderm, Brm-null cells subsequently shifted identities, predominantly becoming neural precursors, violating germ layer assignment. Trajectory inference showed sudden acquisition of non-mesodermal identity in Brm-null cells, consistent with a new transition state inducing a saddle-node bifurcation. Mechanistically, loss of Brm prevented de novo accessibility of cardiac enhancers while increasing expression of the neurogenic factor POU3F1 and preventing expression of the neural suppressor REST. Brm mutant identity switch was overcome by increasing BMP4 levels during mesoderm induction, repressing Pou3f1 and re-establishing a cardiogenic chromatin landscape. Our results reveal BRM as a compensable safeguard for fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory that must be safeguarded.

2021-10-27 | GSE150180 | GEO

Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis.

Project description:Chromatin remodeling complexes instruct cellular differentiation and lineage specific transcription. The BRG1/BRM-associated factor (BAF) complexes are important for several aspects of differentiation. We show that the catalytic subunit gene Brg1 has a specific role in cardiac precursors (CPs) to initiate cardiac gene expression programs and repress non-cardiac expression. Using immunopurification with mass spectrometry, we have determined the dynamic composition of BAF complexes during mammalian cardiac differentiation, identifying several cell-type specific subunits. We focused on the CP- and cardiomyocyte (CM)-enriched subunits BAF60c (SMARCD3) and BAF170 (SMARCC2). Baf60c and Baf170 co-regulate gene expression with Brg1 in CPs, and in CMs their loss results in broadly deregulated cardiac gene expression. BRG1, BAF60c and BAF170 modulate chromatin accessibility, to promote accessibility at activated genes while closing chromatin at repressed genes. BAF60c and BAF170 are required for proper BAF complex composition, and BAF170 loss leads to retention of BRG1 at CP-specific sites. Thus, dynamic interdependent BAF complex subunit assembly modulates chromatin states and thereby participates in directing temporal gene expression programs in cardiogenesis.

| S-EPMC6803373 | biostudies-literature

Chromatin remodeler Brahma safeguards canalization in cardiac mesoderm differentiation [ATAC-seq]

Project description:We performed ATAC-seq on WT and BRM KO ESCs and D2 EBs in 3 biological replicates follwing Corces et al., 2017 paper.

2021-10-27 | GSE177480 | GEO

Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis [RNA-Seq II]

Project description:We performed differential mRNA analysis in WT and BRG1 KO cells during cardiac precursor and cardiomyocytes stages of directed differention of mouse ES cells to cardiac myocytes. We show that BRG1 activity is higher in cardiac precursor cells and severely reduced in cardiac myocytes

2019-02-28 | GSE116286 | GEO

Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis

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

2019-02-28 | GSE116296 | GEO

Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis

Project description:Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis

| PRJNA478046 | ENA

RNA-seq data: Baf60c homozygous deletion vs. WT at two time points in cardiac differentiation

Project description:This project compares Baf60c homozygous deletions to WT at two time points during cardiac differentiation. This data is used in two separate projects: first to assess the role of Baf60c in regulating cardiac gene expression, and second to assess the repeatability of results from different RNA-seq analysis tools. There are 12 samples total; 3 replicates for each group, times 2 genetic backgrounds (WT and Baf60c homozygous KO), times two timepoints (cardiomyocyte (D10) and cardiac precusor (D5.3)).

2014-08-10 | E-GEOD-59383 | biostudies-arrayexpress

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