Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin immunoprecipitation of S. pombe followng nitrogen startvation to identfy binding sites of histone H3 C-terminus, H3K9ac and H4K5ac

ABSTRACT: Nitrogen starvation in the fission yeast yeast Schizosaccharomyces pombe causes nucleosome depletion in both promoters and coding regions of activated genes

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Jakub Orzechowski Westholm

PROVIDER: E-TABM-785 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes.

Kristell Carolina C Orzechowski Westholm Jakub J Olsson Ida I Ronne Hans H Komorowski Jan J Bjerling Pernilla P

Genome research 20100119 3

Gene transcription is associated with local changes in chromatin, both in nucleosome positions and in chemical modifications of the histones. Chromatin dynamics has mostly been studied on a single-gene basis. Those genome-wide studies that have been made primarily investigated steady-state transcription. However, three studies of genome-wide changes in chromatin during the transcriptional response to heat shock in the budding yeast Saccharomyces cerevisiae revealed nucleosome eviction in promote ...[more]

PMID: 20086243

Similar Datasets

Chromatin immunoprecipitation to identify Ino80 binding sites in yeast following phosphate startvation

Project description:ChIP on CHIP analysis were performed to analyse the direct involvement of Ino80 in the regulation of the phosphate responsive and nucleotide metabolism genes upon phosphate starvation: We immunoprecipitated Ino80-bound chromatin fragments after formaldehyde crosslinking from cells grown in minimal medium (EMM) or minimal medium lacking phosphate and purified, amplified and probed the Ino80-associated DNA using oligonucleotide tiling arrays.

2009-12-14 | E-MEXP-2284 | biostudies-arrayexpress

An effective approach for identification of in vivo proteinM-bM-^@M-^SDNA binding sites from paired-end ChIP-Seq data

Project description:ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of proteinM-bM-^@M-^SDNA interactions in-vivo in the genome. In general, current algorithms for ChIP-seq reads employ artificial estimation of the average length of DNA fragments for peak finding, leading to uncertain prediction of DNA-protein binding sites. Here, we present SIPeS (Site Identification from Paired-end Sequencing), a novel algorithm for precise identification of binding sites from short reads generated from paired-end Solexa ChIP-Seq technology. SIPeS uses a dynamic baseline directly via M-bM-^@M-^Xpiling upM-bM-^@M-^Y the corresponding fragments defined by the paired reads to efficiently find peaks corresponding to binding sites. The performance of SIPeS is demonstrated by analyzing the ChIP-Seq data of the Arabidopsis basic helix-loop-helix transcription factor ABORTED MICROSPORES (AMS). The robustness of SIPeS was demonstrated in higher sensitivity and spatial resolution in peak finding compared to three existing peak detection algorithms. Keywords: transcription factors (protein-DNA interactions) Examination of protein-DNA interactions in buds of Arabidopsis anther cell

2010-06-04 | E-GEOD-16940 | biostudies-arrayexpress

ChIP-sequencing of Snai1 transcription factor in triple negative breast cancer cell line Hs578T

Project description:This experiment is performed to reveal the novel binding sites of Snai1 transcription factor globally in triple negative breast cancer cell line Hs578T. We also reveal the effect of TGF cytokine on the binding sites of Snai1.

2018-04-25 | E-MTAB-5242 | biostudies-arrayexpress

ChIP-sequencing of ZEB1 in triple negative breast cancer cell line Hs578T

Project description:This experiment is performed to reveal the novel binding sites of ZEB1 transcription factor globally in triple negative breast cancer cell line Hs578T. We also reveal the effect of TGF cytokine on the binding sites of ZEB1.

2018-04-25 | E-MTAB-5241 | biostudies-arrayexpress

Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe [ChIP-Seq data]

Project description:Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway leading to the expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway. The genes induced by phosphate limitation and the molecular mechanism by which the genetically identified positive (pho7+) and negative (csk1+) regulators function are not known. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response for the ScPHO5 (pho1+), ScPHO84 (spbc8e4.01c+), and ScGIT1 (spbc1271.09+) orthologs. We use ChIP-Seq to identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. We provide a global analysis of the PHO pathway in S. pombe. Our results elucidate the conserved core regulon required for responding to phosphate starvation between distantly related ascomycetes and a better understanding of flexibility in environmental stress response networks. ChIP Sequencing of the Schizosaccharomyces pombe 972h- transcription factor Pho7-TAP in high-Pi, no-Pi, and csk1M-NM-^T conditions

2013-01-02 | E-GEOD-39498 | biostudies-arrayexpress

Genome-wide mapping of immature erythrocyte transcribed chromosomal domains (F1-seq)

Project description:Transcriptional regulation is impacted by multiple layers of genome organization. Here, we identified and mapped out all the transcriptionally active chromosomal domains in the chicken immature erythrocyte genome, including the known Î²- and Î±-globin domains, by combining a powerful chromatin fractionation method with next generation DNA and RNA sequencing. To characterize transcriptionally active chromatin domains, we used two biological replicates. Each replicate set has one control SE fraction and one transcriptionally active chromatin fraction (F1)

2016-07-03 | E-GEOD-75849 | biostudies-arrayexpress

The chicken erythrocyte epigenome

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

2016-07-03 | E-GEOD-75955 | biostudies-arrayexpress

Identification of CEBPA and RUNX1 interactors in 3q-rearranged AML (HNT-34)

Project description:Chromatin immunoprecipitation with specific isolation of chromatin associated proteins (ChIP-SICAP) was used to identify chromatin-bound interactors of CEBPA and RUNX1 in the 3q-rearranged human myeloid leukemia cell line HNT-34.

2021-04-29 | PXD020054 | Pride

Identification of CEBPA and RUNX1 interactors in 3q-rearranged AML (MOLM-1)

2021-04-29 | PXD020050 | Pride

Identification of CEBPA and RUNX1 interactors in 3q-rearranged AML

2021-04-29 | PXD020045 | Pride