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

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

ABSTRACT: Sequencing of mononucleosomal DNA during asynchronous mitosis and 0, 3 and 5 hours into meiosis in Schizosaccharomyces pombe. Two samples from mononucleosomal DNA from asynchronous mitosis (haploid 972 h- and diploid pat1.114) and three samples from 0, 3 and 5 hours into meiosis (from diploid pat1.114) were sequenced (Illumina Genome Analyzer IIx) using the single-end read protocol.

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Luis Quintales

PROVIDER: E-GEOD-41772 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe.

Soriano Ignacio I Quintales Luis L Antequera Francisco F

BMC genomics 20131121

<h4>Background</h4>Nucleosomes facilitate the packaging of the eukaryotic genome and modulate the access of regulators to DNA. A detailed description of the nucleosomal organization under different transcriptional programmes is essential to understand their contribution to genomic regulation.<h4>Results</h4>To visualize the dynamics of individual nucleosomes under different transcriptional programmes we have generated high-resolution nucleosomal maps in Schizosaccharomyces pombe. We show that 98 ...[more]

PMID: 24256300

Similar Datasets

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis in Schizosaccharomyces pombe, Schizosaccharomyces octosporus, Schizosaccharomyces japonicus and Saccharomyces cerevisiae Samples from mononucleosomal DNA from asynchronous mitosis of four species of budding (Saccharomyces cerevisiae W303-1a) and fission yeasts (S. pombe wild type 972h-, S. octosporus CBS1804, S. japonicus var. japonicus ade12- FY53) were sequenced (Illumina Genome Analyzer IIx and HiSeq 2500) using the single read and paired end protocol.

2015-04-10 | E-GEOD-52170 | biostudies-arrayexpress

Promoter nucleosome dynamics regulated by signaling through the CTD code

Project description:Sequencing of mononucleosomal DNA from asynchronous cells of Schizosaccharomyces pombe WT and S2A mutant Mononucleosomal DNA from asynchronous S. pombe WT (1 sample) and S2A mutant cells (2 samples) were sequenced (Illumina HiSeq 2000) using the single-end read protocol

2015-06-22 | E-GEOD-59768 | biostudies-arrayexpress

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

Project description:Mononucleosomal DNA analysis of atf1D and pcr1D mutants of Schizosaccharomyces pombe and transcription analysis of exponential wild type 972 h-, atf1D, pcr1D and mitotic diploid pat1.114, and synchronous diploid pat1.114 at 0h, 3h and 5h into meiosis Mononucleosomal DNA vs. genomic input DNA in wildtype 972 h-, atf1D and pcr1D mutants of S. pombe was hybridized to Affymetrix GeneChip 1.0FR tiling microarrays (GPL7715). Total RNA for genome-wide transcription analysis from exponential wild type 972 h-, atf1D, pcr1D and mitotic diploid pat1.114 cells, and from synchronous diploid pat1.114 at 0h, 3h and 5h into meiosis was hybridized to the same microarrays.

2013-11-25 | E-GEOD-41770 | biostudies-arrayexpress

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

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

2013-11-25 | E-GEOD-41773 | biostudies-arrayexpress

Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (MNase)

Project description:Nucleosome occupancy (NO) profiling in fission yeast Schizosaccharomyces pombe Agilent 60mer array was used to analyze mononucleosomal DNA recovered by MNase treatment from asynchronous culture of fission yeast.

2011-01-07 | E-GEOD-25600 | biostudies-arrayexpress

Different nucleosomal landscapes at early and late replicating origins in Saccharomyces cerevisiae

Project description:Sequencing of mononucleosomal DNA during G1 and S phases in Saccharomyces cerevisiae Samples from mononucleosomal DNA from WT and rpd3 mutant strains (W303-1a background) in G1 or in S phase in the presence of 0.2 M HU were sequenced (Illumina Genome Analyzer IIx) using the single-end read protocol

2014-09-09 | E-GEOD-54377 | biostudies-arrayexpress

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

2015-04-10 | GSE52170 | GEO

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe [NGS_Illumina]

Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis and 0, 3 and 5 hours into meiosis in Schizosaccharomyces pombe.

2013-11-25 | GSE41772 | GEO

Nucleosome eviction in mitosis assists condensin loading and chromosome condensation

Project description:The experiment was performed to assess the importance of nucleosome eviction for the binding of condensin to chromatin during mitosis. The condensin complex associates with chromatin during mitosis to ensure chromosome condensation and accurate segregation, but how this binding is achieved remains poorly understood. Our study indicates that transcription co-activators Gcn5 and Mst2 assist condensin binding during mitosis by evicting nucleosomes. To reach this conclusion, we mapped nucleosomes, during mitosis, in wild-type and gcn5mst2 mutant strains. This experiment allowed us (1) to identify nucleosome-depleted regions (ndrs) during mitosis and to show that condensin tends to colocalize with ndr at the 3ends of genes, and (2) to confirm the importance of nucleosome eviction from ndrs by gcn5 and mst2, during mitosis, for the binding of condensin to chromatin.this experiment determines the patterns of nucleosomes in wild type and mutant fission yeast cells arrested in early mitosis. We analysed wild-type cells, cells lacking Gcn5 histone acetylatransferase (gcn5D) and cells lacking both Gcn5 and Mst2 histone acetyltransferases (Gcn5Dmst2D). All cells used in this study expressed a GFP-tagged version of condensin (Cnd2-GFP) and were blocked in early mitosis at 19C by the nda3-KM311 mutation. Mitotic indexes were determined by scoring the accumulation of Cnd2-GFP in the nucleus. Mitotic cells were collected and chromatin was digested by increasing amount of MNase to produce mononucleosomes. Mononucleosomal DNA was purified on an agarose gel and sequence on an Illumina Nextseq 500 apparatus. Three replicates of wild type, gcn5D and gcn5Dmst2D were analysed. Nucleosome patterns were determined in wild-type cells, cells lacking Gcn5 and cells lacking both Gcn5 and Mst2.

2016-04-18 | E-MTAB-4620 | biostudies-arrayexpress

The conserved role of the RSC chromatin remodeler in the establishment of nucleosome depleted regions

Project description:The occupancy of nucleosomes governs access to the eukaryotic genomes and results from a combination of biophysical features and the effect of ATP-dependent remodeling complexes. Most promoter regions show a conserved pattern characterized by a nucleosome-depleted region (NDR) flanked by nucleosomal arrays. The conserved RSC remodeler was reported to be critical to establish NDR in vivo in budding yeast but other evidences suggested that this activity may not be conserved in fission yeast. By reanalysing and expanding previously published data, we propose that NDR formation is dependent on RSC in both yeast species. We also discuss the most prominent biological role of RSC and the possibility that non-essential subunits define alternate versions of the complex. Samples from mononucleosomal DNA from S. pombe strains h- kanR-tetO-snf21-Tap-natR ura4::rTetR-tup11 were sequenced (Illumina NextSeq 500 platform) using the pair-end read protocol

2016-08-24 | E-GEOD-84912 | 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