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Drosophila melanogaster

ABSTRACT: Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in D. melanogaster [MNase]

PROVIDER: PRJNA284755 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2038260_1.fastq.gz	Fastqsanger.gz
	SRR2038260_2.fastq.gz	Fastqsanger.gz
	SRR2038270_1.fastq.gz	Fastqsanger.gz
	SRR2038270_2.fastq.gz	Fastqsanger.gz
	SRR2038280_1.fastq.gz	Fastqsanger.gz

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Drosophila melanogaster

Project description:Genome-wide profiling of nucleosome sensitivity and chromatin accessibility to MNase in D. melanogaster [RNA-seq]

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Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in D. melanogaster [MNase]

Project description:Nucleosome structure and positioning play pivotal roles in gene regulation, DNA repair and other essential processes in eukaryotic cells. Nucleosomal DNA is thought to be uniformly inaccessible to DNA binding and processing factors, such as MNase. Here, we show, however, that nucleosome accessibility and sensitivity to MNase varies. Digestion of Drosophila chromatin with two distinct concentrations of MNase revealed two types of nucleosomes: sensitive and resistant. MNase-resistant nucleosome arrays are less accessible to low concentrations of MNase, whereas MNase-sensitive arrays are degraded by high concentrations. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C containing dinucleotides. In contrast, MNase-sensitive nucleosomes form on A/T rich sequences represented by transcription start and termination sites, enhancers and DNase hypersensitive sites. Lowering of cell growth temperature to ~10°C stabilizes MNase-sensitive nucleosomes suggesting that variations in sensitivity to MNase are related to either thermal fluctuations in chromatin fiber or the activity of enzymatic machinery. In the vicinity of active genes and DNase hypersensitive sites nucleosomes are organized into synchronous, periodic arrays. These patterns are likely to be caused by “phasing” nucleosomes off a potential barrier formed by DNA-bound factors and we provide an extensive biophysical framework to explain this effect. Mnase-seq, Mnase-ChIP-seq of Drosophila melanogaster embryo and S2 cells chromatin

2015-09-17 | E-GEOD-69177 | biostudies-arrayexpress

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility to MNase in D. melanogaster [RNA-seq]

2015-09-17 | E-GEOD-69335 | biostudies-arrayexpress

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in D. melanogaster

Project description:Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in D. melanogaster

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Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in D. melanogaster [MNase]

2015-09-17 | GSE69177 | GEO

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility to MNase in D. melanogaster [RNA-seq]

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Drosophila melanogaster

Project description:ATAC-seq analysis of chromatin accessibility and nucleosome positioning in Drosophila melanogaster precellular blastoderm embryos

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Project description:Chromatin accessibility in populations of Drosophila melanogaster

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Genome-wide chromatin reconstitution with Drosophila embryo extract and nucleosome positioning by CG7372 and su(Hw)

Project description:We have reconstituted chromatin in vitro on a genome-wide level by incubating total genomic Drosophila melanogaster DNA in D. melanogaster preblastoderm embryo extract. We analyzed chromatin reconstituted with 1) extract from wildtype embryos, 2) extract from embryos lacking the chromatin remodeling enzyme subunit Acf , and 3) extract from Acf-mutant embryos supplemented with recombinant ACF (Acf + Iswi). As a comparison, we also reconstituted chromatin on genomic DNA by salt gradient dialysis. We determined nucleosome positions in reconstituted chromatin by MNase-digestion followed by paired-end sequencing of mononucleosomal fragments. We also determined nucleosome positions in D. melanogaster BG3-c2 cells depleted for the proteins su(Hw) and CG7372 by RNA interference.

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Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos[ChIP-Seq]

Project description:H1 ChIP-seq profiling and nucleosome MNase-seq profiling were performed in after egg laying (AEL) 3-4 hours (hr) and 14-15hr Drosophila melanogaster embryos (W1118).

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