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Chromatin remodeler Brahma safeguards canalization of a labile epigenomic state in precardiac mesoderm[scRNA-Seq]

ABSTRACT: We perfromed single cell RNA Seq of WT and BRM KO cells at mesoderma nd cardiac myocyte stages of cardiac differentiation

ORGANISM(S): Mus musculus

PROVIDER: GSE116293 | GEO | 2022/01/31

REPOSITORIES: GEO

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Chromatin remodeler Brahma safeguards labile canalization of cardiac mesoderm differentiation

Project description:Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization. Canalization is essential for stabilizing cell fate, but mechanisms underlying robust canalization are unclear. Here we show that the BRG1/BRM-associated factor (BAF) chromatin remodeling complex ATPase gene Brm safeguards cell identity during directed cardiogenesis of mouse embryonic stem cells. Despite establishment of well-differentiated precardiac mesoderm, Brm-null cells predominantly became 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 referred to as a saddle-node bifurcation. Mechanistically, loss of Brm prevented de novo accessibility of cardiac enhancers while increasing expression of neurogenic factor POU3F1, preventing expression of neural suppressor REST, and disrupting composition of BRG1 complexes. Brm mutant identity switch was overcome by increasing BMP4 levels during mesoderm induction. Mathematical modeling supports all our observations. In the mouse embryo, Brm deletion exacerbated mesoderm-deleted Brg1 mutant phenotypes, severely compromising cardiogenesis, unmasking an in vivo role for Brm. Our results reveal Brm as a compensable safeguard of the fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory.

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

Project description:We compared differential gene expression between WT and BRM KO in mesoderm, cardiac precursors and cardiomyocytes

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

Project description:We used antibody against REST protein (Sigma, 17-10456) to chromatin IP REST at D4 and D6 of cardiac differentiation from WT and BRM KO cells.

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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.

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Brahma safeguards canalization of cardiac mesoderm differentiation.

Project description:Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization1,2. Canalization is essential for stabilizing cell fate, but the mechanisms that underlie robust canalization are unclear. Here we show that the BRG1/BRM-associated factor (BAF) chromatin-remodelling complex ATPase gene Brm safeguards cell identity during directed cardiogenesis of mouse embryonic stem cells. Despite the establishment of a well-differentiated precardiac mesoderm, Brm-/- cells predominantly became neural precursors, violating germ layer assignment. Trajectory inference showed a sudden acquisition of a non-mesodermal identity in Brm-/- cells. Mechanistically, the loss of Brm prevented de novo accessibility of primed cardiac enhancers while increasing the expression of neurogenic factor POU3F1, preventing the binding of the neural suppressor REST and shifting the composition of BRG1 complexes. The identity switch caused by the Brm mutation was overcome by increasing BMP4 levels during mesoderm induction. Mathematical modelling supports these observations and demonstrates that Brm deletion affects cell fate trajectory by modifying saddle-node bifurcations2. In the mouse embryo, Brm deletion exacerbated mesoderm-deleted Brg1-mutant phenotypes, severely compromising cardiogenesis, and reveals an in vivo role for Brm. Our results show that Brm is a compensable safeguard of the fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory.

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Brahma safeguards canalization of cardiac mesoderm differentiation

Project description:Brahma safeguards canalization of cardiac mesoderm differentiation

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Brahma safeguards canalization of cardiac mesoderm differentiation

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

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

Project description:Chromatin remodeler Brahma safeguards canalization in cardiac mesoderm differentiation [RNA-seq]

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

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