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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ATAC-Seq]

ABSTRACT: Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ATAC-Seq]

PROVIDER: PRJNA490021 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7811570.fastq.gz	Fastqsanger.gz
	SRR7811580.fastq.gz	Fastqsanger.gz
	SRR7811571.fastq.gz	Fastqsanger.gz
	SRR7811572.fastq.gz	Fastqsanger.gz
	SRR7811573.fastq.gz	Fastqsanger.gz

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [chromatin-associated RNA-Seq]

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ATAC-Seq]

Project description:Dynamic control of the accessibility of the genomic regulatory information is at the heart of stimulus-induced gene expression changes. Whereas chromatin accessibility assays describe dynamic changes in open chromatin over time, they provide only indirect and limited information on the nucleosome remodeling events that underlie such changes. Here, we combined accessibility assays and ChIP-seq on nucleosomes generated by micrococcal nuclease digestion in resting and LPS-activated macrophages. We devised a novel quantitative framework to discriminate different types of nucleosome remodeling events and used it to analyze nucleosome organization at genomic cis-regulatory elements modulated by stimulation on a genomic scale. At typical stimulus-activated enhancers, remodeling events were commonly asymmetric, with only one of the two nucleosomes flanking the central accessible region being remodeled. A systematic analysis of nucleosome organization revealed distinct associations of individual TFs with remodeling and showed that most remodeling events tended to occur early in the response and to be maintained over time, with progressively fewer novel events occurring at later times.

2019-08-01 | GSE119690 | GEO

Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ChIP-Seq]

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [chromatin-associated RNA-Seq]

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages

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

2019-08-01 | GSE119693 | GEO

Characterization of cis-regulatory elements of effector ISGs

Project description:We investigated the transcriptional activation and cis-regulatory elements of effector ISGs in CD8+ murine dendritic cells (DCs) stimulated with IFN-beta. We analysed gene repression changes and characterized activated cis-regulatory regions. Binding of ISGF3 subunits (IRF9, Stat1, and Stat2) and other transcription factors, DNA motifs, and chromatin status were also determined.

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Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells.

Project description:Accessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). While stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of cis-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) data sets and used it to analyze nucleosome dynamics at stimulus-regulated cis-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing, however, different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.

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Msn2-mediated nucleosome remodeling dynamics

Project description:Msn2-mediated nucleosome remodeling dynamics

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