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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE119693 | GEO | 2019/08/01

REPOSITORIES: GEO

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Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ChIP-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 | GSE119691 | GEO

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

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

| PRJNA490020 | ENA

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

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

| PRJNA490021 | ENA

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

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

| PRJNA490019 | ENA

Integrative dissection of gene regulatory elements at base resolution

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

2022-12-31 | GSE206377 | GEO

High-throughput discovery of post-transcriptional cis-regulatory elements

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

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In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering.

Project description:RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs. We use GenERA to survey the entire regulatory landscape of a 3'UTR, and apply it in a multiplex fashion to analyse combinatorial interactions between sets of miRNA response elements (MREs), providing strong evidence for cooperative activity. We also employ this technology to probe the functionality of an entire MRE network under cellular homeostasis, and show that high-resolution analysis of the GenERA dataset can be used to extract functional features of MREs. This study provides a genome editing-based multiplex strategy for direct functional interrogation of RNA cis-regulatory elements in a native cellular environment.

| S-EPMC5727397 | biostudies-literature

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