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Mus musculus

ABSTRACT: Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq]

PROVIDER: PRJNA175501 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR572702_1.fastq.gz	Fastqsanger.gz
	SRR572702_2.fastq.gz	Fastqsanger.gz
	SRR572703_1.fastq.gz	Fastqsanger.gz
	SRR572703_2.fastq.gz	Fastqsanger.gz
	SRR572704_1.fastq.gz	Fastqsanger.gz

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Genome-wide nucleosome positioning during embryonic stem cell development

Project description:This SuperSeries is composed of the following subset Series: GSE40910: Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq] GSE40948: Genome-wide nucleosome positioning during embryonic stem cell development [RNA-Seq] GSE40951: Genome-wide nucleosome positioning during embryonic stem cell development [ChIP-Seq] Refer to individual Series

2012-10-21 | E-GEOD-40896 | biostudies-arrayexpress

Mus musculus

Project description:Genome-wide nucleosome positioning during embryonic stem cell development [ChIP-Seq]

| PRJNA175503 | ENA

Mus musculus

Project description:Genome-wide nucleosome positioning during embryonic stem cell development [RNA-Seq]

| PRJNA175502 | ENA

Genome-wide nucleosome positioning during embryonic stem cell development

Project description:Genome-wide nucleosome positioning during embryonic stem cell development

| PRJNA175500 | ENA

Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [MNase-seq]

Project description:We utilized MNase-seq to profile nucleosome positions in wild type (Ax2) and ChdC null cells both in growing cells and a partially developed state (loose-mound) to study changes in nucleosome positioning and occupancy during development and the impact the deletion of ChdC an ATP-dependent chromatin remodeller has on nucleosome positioning and occupancy. As a control for MNase sequence bias we also digested naked DNA with MNase.

2017-02-26 | GSE70122 | GEO

The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells

Project description:Nucleosome remodeling factors regulate the occupancy and positioning of nucleosomes genome-wide through ATP-driven DNA translocation. While many nucleosomes are well- and consistently positioned, some nucleosomes and nucleosome-like structures are more sensitive to nuclease digestion or transitory in nature. To better understand the role of nucleosome remodeling factors in generating and clearing these alternative nucleosome structures, we depleted murine embryonic stem cells of the remodeler ATPases BRG1 and SNF2H then performed MNase-seq in murine embryonic stem cells. We performed MNase-seq under high- and low-MNase conditions to assess the effects of nucleosome remodeling factors on nuclease-sensitive or “fragile” nucleosome occupancy. In parallel, we gel-extracted MNase-digested fragments to enrich for another alternative nucleosome structure, the overlapping dinucleosome. Overlapping dinucleosomes are composed of two canonical nucleosomes, asymmetrically lacking one H2A:H2B dimer and wrapped by ~250 bp of DNA. In vitro studies of nucleosome remodeling have suggested that the collision of adjacent nucleosomes by nucleosome sliding can stimulate formation of overlapping dinucleosomes. Using these methods, we were able to identify fragile nucleosomes and overlapping dinucleosomes near transcription start sites and gene-distal DNaseI hypersensitive sites in mouse embryonic stem cells, among other loci. We find that BRG1 consistently stimulates occupancy of fragile nucleosomes but represses occupancy of overlapping dinucleosomes through its nucleosome remodeling function, while SNF2H expression slightly increases fragile nucleosome occupancy.

2023-03-14 | GSE216057 | GEO

Nucleosome positioning changes during human embryonic stem cell differentiation

Project description:Nucleosome positioning changes during human embryonic stem cell differentiation

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Homo sapiens

Project description:Nucleosome positioning changes during human embryonic stem cell differentiation.

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Mus musculus

Project description:Whole genome nucleosome positioning by MNase-Seq on the mouse tumor line, RMA

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Dynamic nucleosome remodeling mediated by YY1 underlies early mouse development

Project description:Nucleosome positioning can alter the accessibility of DNA-binding proteins to their cognate DNA elements, and thus its precise control is essential for cell identity and function. Mammalian preimplantation embryos undergo temporal changes in gene expression and cell potency, suggesting the involvement of dynamic epigenetic control during this developmental phase. However, the dynamics of nucleosome organization during early development are poorly understood. In this study, using a low-input MNase-seq method, we show that nucleosome positioning is globally obscure in zygotes but becomes well defined during subsequent development. Downregulation of the chromatin assembly in embryonic stem cells can partially reverse nucleosome organization into a zygote-like pattern, suggesting that the chromatin assembly pathway might be linked to fuzzy nucleosomes in zygotes. We also reveal that YY1, a zinc finger containing transcription factor expressed upon zygotic genome activation, regulates the de novo formation of well-positioned nucleosome arrays at the regulatory elements, through identifying YY1-binding sites in 8-cell embryos. The YY1-binding regions acquire H3K27ac enrichment around the 8-cell and morula stages and YY1 depletion impairs the morula-to-blastocyst transition. Thus, our study delineates the remodeling of nucleosome organization and its underlying mechanism during early mouse development.

2023-07-16 | GSE220074 | GEO

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