Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

BAR-ChIP on yeast chromatin associated mutants

ABSTRACT: We have profiled various H3 post-translational modifications in a wide range of chromatin-associated mutants in yeast. Those include H3K14ac, H3K4me3, H3K4me2, H3K4me1 and H3K36me3.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-2945 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-11-10 | E-GEOD-73554 | biostudies-arrayexpress

Genetic differences underlying chromatin discordance between monozygotic twins [FAIR-seq]

Project description:Open chromatin is implicated in regulatory processes, and thus variation in chromatin structure may contribute to variation in gene expression and other molecular phenotypes. In this work, we performed a targeted deep sequencing to identify somatic mutations and genetic polymorphisms underlying accessible chromatin in the genomes of 72 monozygotic twins. Open chromatin sequencing based on FAIRE assay for 36 pairs of monozygotic twins

2014-03-24 | E-GEOD-44742 | biostudies-arrayexpress

Genetic differences underlying chromatin discordance between monozygotic twins

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-03-24 | E-GEOD-53823 | biostudies-arrayexpress

Nucleosome Mapping in S. pombe Centromeres

Project description:A key element for defining the centromere identity is the incorporation of a specific histone H3, CENP-A, known as Cnp1p in S. pombe. Previous studies have suggested that functional S. pombe centromeres lack nucleosome arrays and may involve chromatin remodeling as a key step of kinetochore assembly. We used tiling microarrays to show that nucleosomes are in fact positioned in regular intervals in the core of centromere 2, providing the first high resolution map of regional centromere chromatin. Nucleosome locations are not disrupted by mutations in kinetochore proteins cnp1, mis18, mis12, nuf2, mal2, overexpression of Cnp1p, or deletion of ams2. Bioinformatic analysis of the centromere sequence indicates certain enriched motifs in linker regions between nucleosomes and reveals a sequence-bias in nucleosome positioning. We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence. In addition, sequence analysis of nucleosome-free regions identifies novel binding sites for the GATA-like protein Ams2p, which participates in CENP-A incorporation. Keywords: Nucleosome Mapping Study Entire cnt regions and histone-related genes were tiled at 1-5 bp spacing using 60-mer probes.

2008-05-30 | E-GEOD-10742 | biostudies-arrayexpress

Determinants of nucleosome positioning and their influence on plant gene expression

Project description:We report the global nuclesome posiitons to study the relationship between nucleosome occupancy and gene expression in response to Coronatine in Arabidopsis We examined nucleosome occupancy and mRNA abundance in response to Coronatine in Arabidopsis rosette leaves

2015-05-27 | E-GEOD-64397 | biostudies-arrayexpress

Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [single-end MNase-seq]

Project description:Experiments performed over the past three decades have shown that nucleosomes are transcriptional repressors. In Saccharomyces cerevisiae, depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds genes. The mechanism of de-repression is hypothesized to be rooted directly in chromatin changes. To test this, we reproduced classical H4 depletion experiments by conditional repression of all histone H3 transcription, which depletes the supply of nucleosomes in vivo. RNA-seq results were consistent with the earlier studies, but much more sensitive, revealing nearly 2500 de-repressed genes. Changes in chromatin organization were determined by MNase-seq. Nucleosomes that were preferentially retained occurred in regions of high DNA-encoded nucleosome affinity, and were marked with H3K36me2, which is linked to transcription elongation. Nucleosomes harboring acetyl marks or that contained the variant histone H2A.z were preferentially lost. Genes that were de-repressed lost or rearranged nucleosomes at their promoter, but not in the gene body. Therefore, a combination of DNA-encoded nucleosome stability and nucleosome composition dictates which nucleosomes will be lost under conditions of limiting histone protein. This, in turn, governs which genes will experience a loss of regulatory fidelity. MNase-seq experiments consist of three wildtype (1 single-end and 2 paired-end) and four mutant (DCB200.1/H3 shutoff; 2 single-end, 2 paired-end) replicates. Each replicate contains two timepoints reflecting chromatin immediately after ("O hours") and 3 hours after transition to media containing dextrose. RNA-seq data includes three replicates from wildtype or H3 depleted cells after 3 hours in media containing dextrose.

2012-09-26 | E-GEOD-29291 | biostudies-arrayexpress

Nucleosome occupancy microarray for WT and jhd2-delete strains though sporulation

Project description:WT (MMY718) and jhd2M-bM-^HM-^F (MMY1879) sporulating cell cultures were profiled for global nucleosome occupancy using Affymetrix high-resolution tiling arrays. MNase-treated mono-nucleosomes from WT and jhd2M-bM-^HM-^F cultures in rich media, and sporulation timepoints at 0h, 4h, 6h, 8h, 10h, 12h, and 16h were microarrayed.

2012-10-01 | E-GEOD-40874 | biostudies-arrayexpress

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse (Mnase-Seq)

Project description:Methylation of cytosines (5meC) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here we use Saccharomyces cerevisiae as a system lacking DNA methylation to define the chromatin features influencing the activity of the murine DNMT3B. Our data demonstrate that DNMT3B and H3K4 methylation are mutually exclusive and that DNMT3B is co-localized with H3K36 methylated regions. In support of this observation, DNA methylation analysis in yeast strains without Set1 and Set2 show an increase of relative 5meC levels at the TSS and a decrease in the gene-body, respectively. We extend our observation to the murine male germline, where H3K4me3 is strongly anti-correlated while H3K36me3 correlates with accelerated DNA methylation. These results show the importance of H3K36 methylation for gene-body DNA methylation in vivo. Nucleosome mapping in yeast

2015-04-02 | E-GEOD-66907 | biostudies-arrayexpress

ChIP-seq of histone H3 and H3K9me2 in WT and dbl2 mutant fission yeast

Project description:The aim was to compare the levels of histone H3 dimethylation at lysine 9 (H3K9me2) in wild-type and dbl2 knock-out Schizosaccharomyces pombe cells. Fission yeast cultures were grown in the complex YES medium to exponential phase and chromatin immunoprecipitation was carried out using anti-H3 and anti-H3K9me2 antibodies. Two independent biological replicates were performed. The resulting IP and input DNA samples were sequenced using Illumina sequencing (35 nt PE). H3K9me2 occupancy in each sample was normalized to the corresponding total H3 occupancy, and normalized H3K9me2 levels were compared between WT and dbl2 knock-out.

2020-10-02 | E-MTAB-9619 | biostudies-arrayexpress

Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint

Project description:Exogenous double-stranded RNA (dsRNA) has been shown to exert homology-dependent effects at the level of both target mRNA stability and chromatin structure. Using C. elegans undergoing RNAi as an animal model, we have investigated the generality, scope, and longevity of chromatin-targeted dsRNA effects and their dependence on components of the RNAi machinery. Using high-resolution genome-wide chromatin profiling, we found that a diverse set of genes can be induced to acquire locus-specific enrichment of H3K9 trimethylation, with modification footprints extending several kilobases from the site of dsRNA homology and with locus specificity sufficient to distinguish the targeted locus from among all 20,000 genes in the C. elegans genome. Genetic analysis of the response indicated that factors responsible for secondary siRNA production during RNAi were required for effective targeting of chromatin. Temporal analysis revealed that H3K9 methylation, once triggered by dsRNA, can be maintained in the absence of dsRNA for at least two generations before being lost. These results implicate dsRNA-triggered chromatin modification in C. elegans as a programmable and locus-specific response defining a metastable state that can persist through generational boundaries. H3K9me3 nucleosome-IP sequencing and small RNA sequencing in C. elegans populations that underwent RNAi

2012-01-06 | E-GEOD-32631 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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