Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Histone acetylation, not stoichiometry, regulates linker histone binding in S. cerevisiae

ABSTRACT: Linker histones play a fundamental role in shaping chromatin structure, but how their interaction with chromatin is controlled not well understood. In this study we used a combination of genetic and genomic approaches to explore the regulation of linker histone binding in the yeast, Saccharomyces cerevisiae. Despite the tight correlation between linker-to-core histone ratio and nucleosome repeat length (NRL) observed in many organisms, we found that increasing Hho1 levels did not change the overall NRL in yeast chromatin. While over-expression of Hho1 did not alter nucleosome spacing, it did result in a severe growth defect, which could be rescued by mutations that increased histone acetylation in the cell. Consistent with this, genome-wide analysis of linker histone occupancy revealed an inverse correlation with histone tail acetylation in both yeast and mouse embryonic stem cells. Collectively these results suggest that histone acetylation negatively regulates linker histone binding in S. cerevisiae and other organisms.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE100591 | GEO | 2017/07/10

SECONDARY ACCESSION(S): PRJNA392237

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)

Project description:Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. Remodelers are also enriched in the bodies of genes displaying high nucleosome turnover. We hypothesize that remodelers bind but do not act at 5' NDRs, remaining in physical proximity to gene bodies, where they act on regions of transient nucleosome depletion following transcriptional elongation. We have analyzed the dynamics of yeast ISWI and CHD chromatin remodeler genomic association at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).

2013-03-01 | E-GEOD-39430 | biostudies-arrayexpress

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)

2013-03-01 | E-GEOD-39431 | biostudies-arrayexpress

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)

2013-03-01 | GSE39431 | GEO

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)

2013-03-01 | GSE39430 | GEO

Chromatin immunoprecipitation to map nucleosomes and H3 lysine 14 acetylation in two unrelated strains of yeast

Project description:Nucleosome mapping and histone H3 lysine 14 acetylation chromatin immuno-precipitation in two unrelated strains of yeast (BY and RM).

2009-08-29 | E-MEXP-1777 | biostudies-arrayexpress

Novel nucleosomal particles containing core histones and linker DNA but no histone H1

Project description:The nucleosome plays a central role in genome regulation. Traditional methods for mapping nucleosomes depend on the resistance of the nucleosome core to micrococcal nuclease (MNase). However, the lengths of the protected DNA fragments are heterogeneous, limiting the accuracy of nucleosome position information. To resolve this problem, we removed residual linker DNA by simultaneous digestion of yeast chromatin with MNase and exonuclease III (ExoIII). Paired-end sequencing of mono-nucleosomes revealed not only core particles (145-147 bp), but also intermediate particles in which ~8 bp project from one side (154 bp) or both sides (161 bp) of the nucleosome core. We term these particles "pseudo-chromatosomes" because they are present in yeast lacking linker histone. They are also observed after MNase-ExoIII digestion of chromatin reconstituted using recombinant core histones. We propose that the pseudo-chromatosome provides a DNA framework to facilitate H1 binding. Comparison of budding yeast nucleosome sequences obtained using micrococcal nuclease (MNase-seq) and MNase + exonuclease III (ExoIII) (MNase-ExoIII-seq): wild type cells and hho1-null cells. Nucleosome sequences from native chromatin and H1-depleted chromatin from mouse liver. Nucleosome sequences from a plasmid reconstituted into nucleosomes using recombinant yeast histones or native chicken erythrocyte histones.

2015-09-23 | E-GEOD-65889 | biostudies-arrayexpress

MEDIATOR subunit med8 binding in Saccharomyces cerevisiae

Project description:The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator – histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis, that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. Med8-TAP strain ChIPed with IgG beads vs. Input in Saccharomyces cerevisiae

2011-11-22 | E-GEOD-28613 | biostudies-arrayexpress

Saccharomyces cerevisiae

Project description:Histone acetylation, not stoichiometry, regulates linker histone binding in S. cerevisiae

| PRJNA392237 | ENA

Novel nucleosomal particles containing core histones and linker DNA but no histone H1

Project description:Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ~147 bp of DNA wrapped ~1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. Micrococcal nuclease (MNase) digests the linker to yield the chromatosome, containing H1 and ~160 bp, and then converts it to a core particle, containing ~147 bp and no H1. Sequencing of nucleosomal DNA obtained after MNase digestion (MNase-seq) generates genome-wide nucleosome maps that are important for understanding gene regulation. We present an improved MNase-seq method involving simultaneous digestion with exonuclease III, which removes linker DNA. Remarkably, we discovered two novel intermediate particles containing 154 or 161 bp, corresponding to 7 bp protruding from one or both sides of the nucleosome core. These particles are detected in yeast lacking H1 and in H1-depleted mouse chromatin. They can be reconstituted in vitro using purified core histones and DNA. We propose that these "proto-chromatosomes" are fundamental chromatin subunits, which include the H1 binding site and influence nucleosome spacing independently of H1.

2015-09-23 | GSE65889 | GEO

Systematic genetic and proteomic screens identify yeast H2BK37 and mammalian H2BK34 methylation as an evolutionary conserved meiotic mark

Project description:Gametes are highly differentiated cells specialized to carry and protect the parental genetic information. Their chromatin organization is highly compacted and the establishment of this nuclear structure involves many chromatin processes. Technical difficulties exclude the analysis of precise histone mutations during mouse spermatogenesis. The model organism Saccharomyces cerevisiae possesses a differentiation pathway named sporulation with striking similarities with mammalian spermatogenesis. This study took advantage of this yeast pathway and performed a systematic mutational screen on the histone H2A and H2B, revealing the residues which are essential for the formation of spores. Many of them are localized on the lateral side of the nucleosome, highlighting the importance of this surface for meiotic divisions and the formation of spores. Second, histones have been purified at different stages of sporulation and their post-translational modifications analyzed by mass spectrometry. Fifteen new sites of acetylation, methylation or phosphorylation have been identified on the core histones in yeast. Methylation of H2BK37 appears to be a new meiotic mark and is important for Rad51 action. Thus, this modification is conserved during mammalian spermatogenesis when it is found enriched during meiosis. Altogether, our results demonstrate that a combination of genetic and proteomic approaches applied to yeast sporulation can reveal new aspects of chromatin signaling pathways during mammalian spermatogenesis.

2020-09-21 | PXD006213 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data