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E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning

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

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE123239 | GEO | 2019/09/25

REPOSITORIES: GEO

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Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning.

Project description:Regulation of chromatin structure is essential for controlling access of DNA to factors that require association with specific DNA sequences. Here we describe the development and validation of engineered chromatin remodeling proteins (E-ChRPs) for inducing programmable changes in nucleosome positioning by design. We demonstrate that E-ChRPs function both in vitro and in vivo to specifically reposition target nucleosomes and entire nucleosomal arrays. We show that induced, systematic positioning of nucleosomes over yeast Ume6 binding sites leads to Ume6 exclusion, hyperacetylation, and transcriptional induction at target genes. We also show that programmed global loss of nucleosome-free regions at Reb1 targets is generally inhibitory with mildly repressive transcriptional effects. E-ChRPs are compatible with multiple targeting modalities, including the SpyCatcher and dCas9 moieties, resulting in high versatility and enabling diverse future applications. Thus, engineered chromatin remodeling proteins represent a simple and robust means to probe and disrupt DNA-dependent processes in different chromatin contexts.

| S-EPMC6884087 | biostudies-literature

E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [MNase-Seq]

Project description:We report the development of a versatile strategy for engineered nucleosome positoining across eukaryotic genomes.

2019-09-25 | GSE123237 | GEO

E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [RNA-Seq]

Project description:We report the development of a versatile strategy for engineered nucleosome positoining across eukaryotic genomes.

2019-09-25 | GSE136021 | GEO

E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [ChIP-Seq]

Project description:We report the development of a versatile strategy for engineered nucleosome positoining across eukaryotic genomes.

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E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning

Project description:E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning

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E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [RNA-Seq]

Project description:E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [RNA-Seq]

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E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [ChIP-Seq]

Project description:E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [ChIP-Seq]

| PRJNA507859 | ENA

E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [MNase-Seq]

Project description:E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [MNase-Seq]

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Nucleosome positioning - Transient Depletion and Recovery of the Essential RSC Chromatin Remodeling Complex

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

2018-12-31 | GSE118214 | GEO

Nucleosome positioning in a model of active chromatin remodeling enzymes.

Project description:Accounting for enzyme-mediated active sliding, disassembly, and sequence-dependent positioning of nucleosomes, we simulate nucleosome occupancy over cell-cycle-scale times using a stochastic kinetic model. We show that ATP-dependent active nucleosome sliding and nucleosome removal processes are essential to obtain in vivo-like nucleosome positioning. While active sliding leads to dense nucleosome filling, sliding events alone cannot ensure sequence-dependent nucleosome positioning: Active nucleosome removal is the crucial remodeling event that drives positioning. We also show that remodeling activity changes nucleosome dynamics from glassy to liquid-like, and that remodeling dramatically influences exposure dynamics of promoter regions.

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