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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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Differential Nucleosome Spacing in Neurons and Glia

Project description:Differential Nucleosome Spacing in Neurons and Glia

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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.

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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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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

Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing

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

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Local and global influences on protein turnover in neurons and glia.

Project description:Proteins exhibit dynamics in their expression level in response to intracellular and extracellular signals. Regulation of protein turnover allows cells to rapidly and efficiently remodel their proteomes. It is known that proteins can show very different turnover rates in different tissue of the same organism, but little is known about protein turnover rates in different brain cell types. We used a dynamic SILAC approach to determine protein half-lives in primary hippocampal cultures (containing a mixture of neurons and glia cells) as well as in neuron-enriched and glia-enriched cultures. We determined the protein half-lives for over 5100 proteins and found half-lives ranging from <1 to > 20 days with a median half-life of 5.4 days in mixed cultures. Membrane proteins as a group were shorter-lived and mitochondrial proteins, surprisingly, were longer-lived. Proteins in glia possessed significantly shorter half-lives than the same proteins in neurons. The presence of glia sped up or slowed down the half-lives of neuronal proteins. Our results demonstrate that both the cell-type of origin as well as the nature of the extracellular environment have potent influences on protein turnover.

2018-06-05 | PXD008596 | Pride

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