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Transcription factor binding and epigenetic modifications during NuRD complex induction

ABSTRACT: Transcription factor binding and epigenetic modifications during NuRD complex induction

PROVIDER: PRJEB26867 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2588250.fastq.gz	Fastqsanger.gz
	ERR2588260.fastq.gz	Fastqsanger.gz
	ERR2588270.fastq.gz	Fastqsanger.gz
	ERR2588280.fastq.gz	Fastqsanger.gz
	ERR2588290.fastq.gz	Fastqsanger.gz

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Transcription factor binding and epigenetic modifications during NuRD complex induction

Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset maps time-resolved DNA association of NuRD complex members, pluripotency factors, components of the RNA polymerase II machinery and changes to histone modifications.

2018-05-31 | E-MTAB-6804 | biostudies-arrayexpress

Nucleosome occupancy during NuRD complex induction

Project description:Nucleosome occupancy during NuRD complex induction

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Nascent transcription during NuRD complex induction

Project description:Nascent transcription during NuRD complex induction

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Transcriptional activity during NuRD complex induction

Project description:Transcriptional activity during NuRD complex induction

| PRJEB26865 | ENA

Nascent transcription during NuRD complex induction

Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset profiles nascent RNA transcription in response to NuRD induction.

2018-05-31 | E-MTAB-6805 | biostudies-arrayexpress

Transcriptional activity during NuRD complex induction

Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset profiles time-resolved transcriptional changes in response to NuRD induction.

2018-05-31 | E-MTAB-6806 | biostudies-arrayexpress

Nucleosome occupancy during NuRD complex induction

Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset identifies genome-wide changes in nucleosome positioning at sites of NuRD association.

2018-05-31 | E-MTAB-6807 | biostudies-arrayexpress

The NuRD chromatin remodelling complex regulates brain cortical development

Project description:Dynamic changes of histone epigenetic modifications and chromatin structure represent an universal mechanism by which cells adapt their transcriptional response to rapidly changing environmental conditions. During neuronal development, extensive chromatin remodeling takes place allowing the transition of pluripotent cells into differentiated neurons. Here we report that the ATP-dependent chromatin remodeling complex NuRD, which couples ATP-dependent nucleosome sliding with histone deacetylase activity, is a major remodeling complex in embryonic brain and plays an instructive role during mouse neuronal development. Importantly, the ATPase subunits of NuRD complex CHD3, CHD4 and CHD5 undergo a functional switch, thereby regulating distinct aspects of neuronal differentiation and migration in a sequential and mostly non-overlapping manner. We conclude that the recruitment of NuRD complexes containing specific CHDs to gene promoters and enhancers plays an instructive role in brain development. Gene expression analysis was performed in the mouse embryonic cortex at three developmental stages: E12.5, E15.5 and E18.5 using total RNA obtained from four embryos for each time point.

2015-06-27 | E-GEOD-70298 | biostudies-arrayexpress

Promoter Decommissioning by the NuRD Chromatin Remodeling Complex Triggers Synaptic Connectivity in the Mammalian Brain

Project description:Precise control of gene expression plays fundamental roles in brain development, but the roles of chromatin regulators in neuronal connectivity have remained poorly understood. Here, we find that depletion of the nucleosome remodeling and deacetylation (NuRD) complex in the cerebellar cortex by in vivo RNAi in rats and conditional knockout of the core NuRD subunit Chd4 in mice profoundly impairs the establishment of granule neuron parallel fiber/Purkinje cell synapses. In RNA-Seq analyses of Chd4 conditional knockout mice, we identify a set of nearly 200 genes that are repressed by the NuRD complex in the cerebellum in vivo. Genome-wide ChIP-Seq analyses reveal that the NuRD complex selectively decommissions the promoters of NuRD-repressed genes in the cerebellum in vivo by inducing the deacetylation of histone H3K9/14 and H3K27 and demethylation of H3K4 at these genes. Importantly, temporal control of promoter decommissioning and repression of NuRD target genes upon maturation of the cerebellum requires the NuRD complex. Finally, in a targeted in vivo RNAi screen of NuRD-repressed target genes, we identify the transcription factor Nhlh1, the RNA-binding protein Elavl2, and the presynaptic regulator Cplx3 as negative regulators of presynaptic differentiation in the cerebellar cortex. Together, these findings define NuRD-dependent promoter decommissioning as a developmentally regulated programming mechanism that releases the brake on presynaptic differentiation and thereby drives synaptic connectivity in the mammalian brain. Three distinct histone modifications using postnatal day 6 or day 22 cerebella from wild type (WT) or Chd4 conditional knockout (cKO) mice were examined in duplicate using libraries prepared with the Illumina ChIP-Seq DNA Sample Prep Kit and sequenced on the Illumina HiSeq 2000 platform.

2014-08-18 | E-GEOD-57758 | biostudies-arrayexpress

CARM1 is an integral component of the NuRD chromatin remodeling complex

Project description:The nucleosome remodeling and deacetylase (NuRD) complex is a large multi-subunit complex that couples ATP-dependent chromatin-remodeling and histone deacetylase activities. Emerging evidence suggested that the NuRD complex is prevalently associated with gene transcriptional activation, but little is known about the underlying molecular mechanisms. Here, we reported that the transcriptional coactivator CARM1 is an integral component of the NuRD complex, expanding the activities of the NuRD complex to include arginine methylation. CARM1-associated NuRD binds and activates a large cohort of genes, including those implicated in cell cycle control, to facilitate the G1/S transition. This gene activation process requires CARM1 to catalyze methylation of histone 3 and a key subunit of the NuRD complex, GATAD2A/2B. The biological significance of this gene activation mechanism is underscored by the coordinated expression of both CARM1 and NuRD in breast cancers, which proves to be critical for breast cancer cell growth in vitro and tumorigenesis in vivo. These findings reveal a gene activation program that requires the dual specificity established by CARM1 on chromatin and a key chromatin remodeler.

2025-05-19 | GSE131863 | GEO

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