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Chip-seq of H3 in murine embryonic stem cells, myotubes and pro-B cells.

ABSTRACT: Nucleosome remodeling results in loss of histone occupancy. To gain insight into variations in H3 occupancy in different murine cell types, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine genome wide occupancy of H3 in ES cells, myotubes and pro-B cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE23830 | GEO | 2010/08/31

SECONDARY ACCESSION(S): PRJNA130639

REPOSITORIES: GEO

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Chip-seq of H3 in murine embryonic stem cells, myotubes and pro-B cells.

Project description:Nucleosome remodeling results in loss of histone occupancy. To gain insight into variations in H3 occupancy in different murine cell types, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine genome wide occupancy of H3 in ES cells, myotubes and pro-B cells. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against total H3 in murine ES cells in normal culture conditions, murine ES cells treated with the TGF-beta inhibitor (SB431542, 10uM) for 24 hours, myotubes differentiated for 48 hours and pro-B cells under normal culture conditions.

2010-08-31 | E-GEOD-23830 | biostudies-arrayexpress

Nucleosome occupancy in wild type and histone H3(A111G) yeast

Project description:We screened for histone H3 mutations that cause derepression of the uninduced CHA1 promoter and identified six mutants, including one, H3(A111G), that causes a constitutively active chromatin configuratin at the uninduced CHA1 promoter. We examined genomewide nucleosome occupancy in the A111G mutant and compared it to wild type yeast; that is the data deposited here. Keywords: Nucleosomal DNA from wild type and histone H3(A111G) mutant yeast

2008-07-19 | GSE12163 | GEO

Characterization of Paf1 complex occupancy in mouse myoblasts and myotubes under control conditions or Phf5a knockdown

Project description:Phf5a regulates occupancy of Paf1 complex in mouse myotubes. In this study we assayed for genome-wide localization of Leo1 subunit of the Paf1 complex in mouse myoblasts or myotubes under conditions of shControl or shPhf5a knockdown. These results revealed that downregualtion of Phf5a results in significant decrease of Leo1 binding to its targets in myotubes.

2016-08-31 | GSE86249 | GEO

H3 ubiquitination by NEDD4 regulates H3 acetylation and

Project description:genome wide occupancy related to H3 ubiquitination at K23/36/37

2017-06-12 | GSE90119 | GEO

Genome-wide expression in asymmetric histone H3 mutants in Saccharomyces cerevisiae

Project description:Using histone H3 mutants designed so that they can only form a heterodimer, we studied the gene expression in a collection of mutants, comparing mutations to one histone H3 tail of a nucleosome compared to two histone H3 tails of a nucleosome.

2020-05-01 | GSE81531 | GEO

FACT activity and histone H3-K56 acetylation promote optimal establishment of chromatin architecture independent of ongoing transcription in Saccharomyces cerevisiae [RNA-Seq]

Project description:FACT is a histone chaperone that can destabilize or assemble nucleosomes. Acetylation of histone H3-K56 weakens a histone:DNA contact that is central to FACT activity, suggesting that this modification could affect FACT functions. We tested this by asking how mutations of H3-K56 and FACT affect nucleosome structure, chromatin integrity, and transcription output. Mimics of unacetylated or permanently acetylated H3-K56 had different effects on FACT in vitro and in vivo as expected, but H3-K56 and FACT mutations caused surprisingly similar changes in transcription of individual genes. Notably, neither the changes in transcript levels nor the effects on nucleosome occupancy resulting from mutations conformed to the model that FACT is needed to overcome nucleosomal barriers during transcription initiation or elongation. Instead, the results suggest that both FACT and H3-K56ac are involved in establishing chromatin architecture prior to transcription and restoring it afterwards. They contribute to a process that optimizes transcription frequency, especially at conditionally expressed genes, and restores chromatin integrity after transcription, especially at the +1 nucleosome to block antisense transcription, but FACT appears to be less involved than expected in directly promoting transcription.

2019-03-06 | GSE118331 | GEO

FACT activity and histone H3-K56 acetylation promote optimal establishment of chromatin architecture independent of ongoing transcription in Saccharomyces cerevisiae [MNase-Seq]

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Nrf2 bindng in C2C12 myotubes

Project description:Nrf2 (NF-E2-related-factor-2) contributes to the maintenance of glucose homeostasis in vivo. Nrf2 suppresses blood glucose levels by protecting pancreatic Î²-cells from oxidative stress and improving peripheral tissue glucose utilization. To elucidate the molecular mechanisms by which Nrf2 contributes to the maintenance of glucose homeostasis, we generated skeletal muscle (SkM)-specific Keap1-knockout (Keap1MuKO) mice that express abundant Nrf2 in SkM and then examined Nrf2-target gene expression in this tissue. In Keap1MuKO mice, blood glucose levels were significantly downregulated, and the levels of glycogen branching enzyme (Gbe1) mRNA, along with those of glycogen branching enzyme (GBE) protein, were significantly upregulated in mouse SkM. Consistent with this result, chemical Nrf2-inducers promoted Gbe1 mRNA expression in both mouse SkM and C2C12 myotubes. Chromatin-immunoprecipitation analysis demonstrated that Nrf2 binds the Gbe1 upstream promoter regions. In Keap1MuKO mice, muscle glycogen content was strongly reduced, and forced GBE expression in C2C12 myotubes promoted glucose uptake. Therefore, our results demonstrate that Nrf2-induction in SkM increases GBE expression and reduces muscle glycogen content, resulting in improved glucose tolerance. Chromatin occupancy of Nrf2 under CDDO-Im-treated condition were generated by deep sequencing, in dupliplicate

2016-04-06 | E-GEOD-78780 | biostudies-arrayexpress

Middle-down MS analysis of intact and clipped histone H3 proteoforms

Project description:There is growing evidence that proteolytic cleavage of histone N-terminal tails, known as histone clipping, influences nucleosome dynamics and functional properties. Using middle-down MS analysis we characterized intact and proteolytically processed histone H3 proteoforms isolated from human hepatocarcinoma cell line HepG2/C3A grown in 3D culture.

2022-03-14 | PXD002535 | Pride

Nucleosome occupancy as a novel chromatin parameter for replication origin functions

Project description:This study defines nucleosome occupancy as a novel parameter for regulating origin activities. Nucleosome occupancy at origins was assessed using histone H3 ChIP-seq during G1 and G2M. Origin activity was determined using BrdU ChIP-seq.

2016-11-14 | GSE81028 | GEO

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