Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [MNase-seq]

ABSTRACT: MNase-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE51599 | GEO | 2014/08/11

SECONDARY ACCESSION(S): PRJNA223672

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [MNase-seq]

Project description:MNase-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells MNase-seq from Drosophila S2 nuclei after CTCF/CP190 or ISWI-specific RNAi treatment

2014-08-11 | E-GEOD-51599 | biostudies-arrayexpress

CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [ChIP-seq]

Project description:H3-ChIP-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells

2014-08-11 | GSE51598 | GEO

CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [ChIP-seq]

Project description:H3-ChIP-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells Histone H3 ChIP-seq from Drosophila S2 cells after CTCF/CP190 or ISWI-specific RNAi treatment

2014-08-11 | E-GEOD-51598 | biostudies-arrayexpress

Quantitative MNase-seq accurately maps nucleosome occupancy levels

Project description:Chromatin mapping using micrococcal nuclease (MNase) has been the standard tool for mapping nucleosomes for >40 years. When coupled with DNA sequencing, MNase-seq can provide base-pair-resolution nucleosome maps. However, determining nucleosome occupancy using MNase-seq has been hampered by its aggressive endo-/exo-nuclease activities, whereby cleavages within linker regions produce oligo- and mono-nucleosomes whereas cleavages within nucleosomes destroy them. Here we introduce a theoretical framework for predicting nucleosome occupancies and an experimental protocol with appropriate spike-in normalization that confirms our theory and provides accurate occupancy levels over an MNase digestion time-course. As expected, DNaseI hypersensitive sites and transcription units are digested by MNase at elevated rates, and the apparent deficiency of nucleosomes at 3’ ends of Drosophila genes is an artifact of MNase preference for AT-rich DNA. Surprisingly, we observed no overall differences between Drosophila euchromatin and heterochromatin, which implies that heterochromatin compaction does not render nucleosomal DNA less accessible than euchromatin.

2019-08-27 | GSE128689 | GEO

Drosophila melanogaster S2 cells nucleosome occupancy data after simulation by heat killed Salmonella typhimurium

Project description:In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, the dynamics of nucleosomes during a genome response has not been well characterized . We stimulated Drosophila S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500. We show widespread nucleosome occupancy change in S2 cells during the immune response, with the biggest nucleosomal loss occurring at 4hr post stimulation.

2014-12-24 | GSE64507 | GEO

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (MNase-seq data sets)

Project description:Remodelers define nucleosome composition, presence and position. Mammalian imitation-switch-type (ISWI) comprise one class, mostly relying on the ATPase Snf2h for activity. We show that embryonic stem cells are viable without Snf2h, enabling to study its function and contrast it to Brg1, the ATPase of SWI/SNF. Loss of Snf2h specifically affects nucleosomal positioning and increases linker lengths genome-wide providing in vivo evidence for ISWI function in ruling nucleosomal spacing. Systematic analysis of transcription factor binding reveals selective requirement on either remodeling activity. One group, containing the transcriptional repressor REST depend on BRG1, while a non-overlapping set including the insulator protein CTCF, relies on Snf2h. Importantly localized reduction in CTCF binding decreases long-range interactions. Collectively, this links mammalian ISWI to nuclear organization, demonstrates its cellular role for nucleosomal periodicity and reveals that transcription factors rely on specific remodeling pathways for proper genomic binding.

2019-04-18 | GSE112134 | GEO

Drosophila melanogaster S2 cells nucleosome occupancy data after simulation by heat killed Salmonella typhimurium

Project description:In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, the dynamics of nucleosomes during a genome response has not been well characterized . We stimulated DrosophilaM-BM- S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500. We show widespread nucleosome occupancy change in S2 cells during the immune response, with the biggest nucleosomal loss occurring at 4hr post stimulation. Drsophila S2 cells at 0hr, 30minutes, 1hr and 4hr post heat-killed Salmonella typhimuriumstimulation

2014-12-24 | E-GEOD-64507 | biostudies-arrayexpress

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

MNase-Seq for nucleosome occupancy

Project description:MNase-Seq for nucleosome occupancy

| PRJNA649224 | ENA