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

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

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE136021 | GEO | 2019/09/25

REPOSITORIES: GEO

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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.

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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 [RNA-Seq]

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

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

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

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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

Mechanism of nucleosome positioning, spacing and regularity in Saccharomyces cerevisiae

Project description:Numerous nucleosome remodeling enzymes tightly regulate nucleosome positions in eukaryotic cells. Transcription and statistical positioning of nucleosomes may also contribute to proper nucleosome organization. Individual contributions remain controversial due to strong redundancy of processes acting on the nucleosome landscape. By incisive yeast genome engineering we radically decreased their redundancy. We find the transcriptional machinery to be disruptive of evenly spaced nucleosomes, and proper nucleosome density critical for their biogenesis. INO80 spaces nucleosomes in vivo and positions the first nucleosome covering genes. It requires its Arp8 and Ies2 subunits, but unexpectedly not the Nhp10 module, for spacing. Whereas H2A.Z stimulates INO80 in vitro, its presence is dispensable for INO80 +1 positioning function in vivo. DNA damage, recombination and transposon integration assays suggest that evenly spaced nucleosomes protect cells against genotoxic stress. We derive a unifying model of the biogenesis of the nucleosome landscape and suggest that it evolved not only to regulate but also to protect the genome.

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Project description:Replication of the eukaryotic genome occurs in the context of chromatin, a nucleoprotein packaging state consisting of repeating nucleosomes. Chromatin is commonly thought to carry epigenetic information from one generation to the next, although it is unclear how such information survives the disruptions of nucleosomal architecture that occur during genomic replication. Here, we sought to directly measure a key aspect of chromatin structure dynamics during replication â?? how rapidly nucleosome positions are established on the newly-replicated daughter genomes. By isolating newly-synthesized DNA marked with the nucleotide analogue EdU, we characterize nucleosome positions on both daughter genomes of budding yeast during a time course of chromatin maturation. We find that nucleosomes rapidly adopt their mid log positions at highly-transcribed genes, and that this process was impaired upon treatment with the transcription inhibitor thiolutin, consistent with a role for transcription in positioning nucleosomes in vivo. Additionally, experiments in the Hir1-delta background reveal a role for HIR in nucleosome spacing. Using strand-specific EdU libraries, we characterize nucleosome positions on the leading and lagging strand daughter genomes, uncovering differences in chromatin maturation dynamics between the two daughter genomes at hundreds of genes. Our data define the maturation dynamics of newly-replicated chromatin, and support a role for transcription in sculpting the chromatin template. Gene expression array.

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