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

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

PROVIDER: PRJNA560960 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10004410_1.fastq.gz	Fastqsanger.gz
	SRR10004410_2.fastq.gz	Fastqsanger.gz
	SRR10004411_1.fastq.gz	Fastqsanger.gz
	SRR10004411_2.fastq.gz	Fastqsanger.gz
	SRR10004412_1.fastq.gz	Fastqsanger.gz

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

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

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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.

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

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

2019-09-25 | GSE123239 | GEO

Nucleosome positioning for 4 yeast species

Project description:Nucleosome positioning for 4 yeast species

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Noncoding RNA-mediated DNA methylation directs nucleosome positioning

Project description:We explored the mechanism by which RdDM affects nucleosome positioning in Arabidopsis thaliana. We showed that POLV has a direct effect on nucleosomes through the SWI/SNF complex. We found that the AGO4-siRNA complex is involved in nucleosome positioning via IDN2. Moreover, the SWI/SNF complex is not required for DNA methylation in positioned nucleosomes. Instead, we found that DNA methylation is needed for nucleosome positioning in differentially methylated regions. Taken together, we propose a model where the RdDM pathway directs nucleosome positioning through DNA methylation to establish transcriptional gene silencing.

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