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Differential Nucleosome Spacing in Neurons and Glia [RNA-seq]

ABSTRACT: Differential Nucleosome Spacing in Neurons and Glia [RNA-seq]

PROVIDER: PRJNA552364 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9637130_1.fastq.gz	Fastqsanger.gz
	SRR9637130_2.fastq.gz	Fastqsanger.gz
	SRR9637131_1.fastq.gz	Fastqsanger.gz
	SRR9637131_2.fastq.gz	Fastqsanger.gz
	SRR9637132_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Differential Nucleosome Spacing in Neurons and Glia

Project description:Differential Nucleosome Spacing in Neurons and Glia

| PRJNA553209 | ENA

Differential Nucleosome Spacing in Neurons and Glia

Project description:Eukaryotic chromosomes are composed of chromatin, in which regularly spaced nucleosomes containing ~147 bp of DNA are separated by linker DNA. Most eukaryotic cells have a characteristic average nucleosome spacing of ~190 bp, corresponding to a ~45 bp linker. However, cortical neurons have a shorter average spacing of ~165 bp. The significance of this atypical global chromatin organization is unclear. We have compared the chromatin structures of purified mouse dorsal root ganglia (DRG) neurons, cortical oligodendrocyte precursor cells (OPCs) and cortical astrocytes. DRG neurons have short average spacing (~165 bp), whereas OPCs (~182 bp) and astrocytes (~183 bp) have longer spacing. We measured nucleosome positions by MNase-seq and gene expression by RNA-seq. Most genes in all three cell types have a promoter chromatin organization typical of active genes: a nucleosome-depleted region at the promoter flanked by regularly spaced nucleosomes phased relative to the transcription start site. In DRG neurons, the spacing of phased nucleosomes downstream of promoters (~178 bp) is longer than expected from the genomic average, whereas phased nucleosome spacing in OPCs and astrocytes is similar to the global average (~183 bp). Thus, the atypical nucleosome spacing of neuronal chromatin does not extend to promoter-proximal regions.

2019-10-07 | GSE133966 | GEO

Differential Nucleosome Spacing in Neurons and Glia [RNA-seq]

2019-10-07 | GSE133745 | GEO

Differential nucleosome spacing in neurons and glia.

Project description:Eukaryotic chromosomes are composed of chromatin, in which regularly spaced nucleosomes containing ∼147 bp of DNA are separated by linker DNA. Most eukaryotic cells have a characteristic average nucleosome spacing of ∼190 bp, corresponding to a ∼45 bp linker. However, cortical neurons have a shorter average spacing of ∼165 bp. The significance of this atypical global chromatin organization is unclear. We have compared the chromatin structures of purified mouse dorsal root ganglia (DRG) neurons, cortical oligodendrocyte precursor cells (OPCs) and cortical astrocytes. DRG neurons have short average spacing (∼165 bp), whereas OPCs (∼182 bp) and astrocytes (∼183 bp) have longer spacing. We measured nucleosome positions by MNase-seq and gene expression by RNA-seq. Most genes in all three cell types have a promoter chromatin organization typical of active genes: a nucleosome-depleted region at the promoter flanked by regularly spaced nucleosomes phased relative to the transcription start site. In DRG neurons, the spacing of phased nucleosomes downstream of promoters (∼182 bp) is longer than expected from the genomic average for DRG neurons, whereas phased nucleosome spacing in OPCs and astrocytes is similar to the global average for these cells (∼183 bp). Thus, the atypical nucleosome spacing of neuronal chromatin does not extend to promoter-proximal regions.

| S-EPMC6943982 | biostudies-literature

Comparative genomics reveals Chd1 as a determinant of nucleosome spacing in vivo

Project description:We generated S.cerevisiae strains in which endogenous copies of candidate nucleosome spacing factors were replaced with the K.lactis copies. With this candidate approach, we found that K.lactis Chd1 directed longer nucleosome repeat length in S.cerevisiae. Generating chimeric proteins revealed that the strongest contribution to this differential spacing lies in the undercharacterised N-terminus of Chd1.

2015-03-18 | GSE66979 | GEO

ACF1 regulates nucleosome spacing in Drosophila euchromatin

Project description:ACF1 regulates nucleosome spacing in Drosophila euchromatin

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Role of Itc1 subnit in ISW2 remodeler in nucleosome positioning and spacing in Saccharomyces cerevisiae

Project description:Role of Itc1 subnit in ISW2 remodeler in nucleosome positioning and spacing in Saccharomyces cerevisiae

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Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing

Project description:Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing

| PRJNA673246 | ENA

The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo

Project description:We addressed the roles of three nucleosome spacing enzymes (ISW1, ISW2 and CHD1) in specifying chromatin organization in S. cerevisiae.

2016-02-17 | GSE69400 | GEO

A role for Snf2 related nucleosome spacing enzymes in genome-wide nucleosome organization

Project description:The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here we show that the combined action of Isw1 and Chd1 nucleosome spacing enzymes is required to maintain this organization. In the absence of these enzymes regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicated that ATP-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome. Examination of nucleosome positioning in mutants of snf2-related enzymes Other data used in this study are provided in GEO Series GSE31301 and GSE31833.

2011-09-16 | E-GEOD-31015 | biostudies-arrayexpress

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