Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of hip1::ura4+ and slm9::ura4+ S. pombe to investigate the role of the HIRA histone chaperone complex

ABSTRACT: The assembly of nucleosomes by histone chaperones is an important component of transcriptional regulation. Here we have assessed the global roles of the S. pombe HIRA histone chaperone complex. Microarray analysis indicates that inactivation of the HIRA complex results in increased expression of at least 4% of fission yeast genes. HIRA-regulated genes overlap with those which are normally repressed in vegetatively growing cells, such as targets of the Clr6 histone deacetylase and silenced genes located in subtelomeric regions. HIRA is also required for silencing of all 13 intact copies of the Tf2 long terminal repeat (LTR) retrotransposon. However, the role of HIRA is not restricted to bona fide promoters, because it also suppresses non-coding transcripts from solo LTR elements and spurious antisense transcripts from cryptic promoters associated with transcribed regions. Furthermore, the HIRA complex is essential in the absence of the quality control provided by nuclear exosome-mediated degradation of illegitimate transcripts. This suggests that HIRA restricts genomic accessibility, and, consistent with this, the chromosomes of cells lacking HIRA are more susceptible to genotoxic agents that cause double strand breaks. Thus the HIRA histone chaperone is required to maintain the protective functions of chromatin.

INSTRUMENT(S): Axon GenePix 4000B scanning hardware

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Heather Murton

PROVIDER: E-MTAB-130 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of fission yeast strains identifies widespread requirement for SWI/SNF and RSC on transcription

Project description:SWI/SNF chromatin remodeling complexes play critical roles in transcription and other chromatin-related processes. The analysis of the two members of this class in Saccharomyces cerevisiae, SWI/SNF and RSC, has heavily contributed to our understanding of these complexes. To understand the in vivo functions of SWI/SNF and RSC in an evolutionarily distant organism, we have characterized these complexes in Schizosaccharomyces pombe. While core components are conserved between the two yeasts, the compositions of S. pombe SWI/SNF and RSC differ from their S. cerevisiae counterparts and in some ways are more similar to metazoan complexes. Furthermore, several of the conserved proteins, including actin-like proteins, are strikingly different between the two yeasts with respect to their requirement for viability. Finally, phenotypic and microarray analyses identified widespread requirements for SWI/SNF and RSC on transcription including strong evidence that SWI/SNF directly represses iron transport genes.

2008-06-13 | E-MTAB-31 | biostudies-arrayexpress

Transcription profiling of fission yeast SAGA mutants shows that the SAGA complex controls the switch from proliferation to sexual differentiation through the opposing roles of its subunits Gcn5 and Spt8

Project description:The SAGA complex is a conserved multifunctional coactivator known to play broad roles in eukaryotic transcription. To gain new insights into its functions, we have performed biochemical and genetic analyses of SAGA in the fission yeast, Schizosaccharomyces pombe. Purification of the S. pombe SAGA complex showed that its subunit composition is identical to that of Saccharomyces cerevisiae. Analysis of S. pombe SAGA mutants revealed that SAGA has two opposing roles regulating sexual differentiation. First, in nutrient rich conditions, the SAGA histone acetyltransferase, Gcn5, represses ste11+, which encodes the master regulator of the mating pathway. In contrast, the SAGA subunit Spt8 is required for the induction of ste11+ upon nutrient starvation. Chromatin immunoprecipitation experiments suggest that these regulatory effects are direct, as SAGA is physically associated with the ste11+ promoter independent of nutrient levels. Genetic tests suggest that nutrient levels do cause a switch in SAGA function, as spt8? suppresses gcn5? with respect to ste11+ derepression in rich medium, whereas the opposite relationship, gcn5? suppression of spt8?, occurs during starvation. Thus, SAGA plays distinct roles in the control of the switch from proliferation to differentiation in S. pombe through the dynamic and opposing activities of Gcn5 and Spt8.

2008-11-19 | E-MTAB-53 | biostudies-arrayexpress

Comparative genomic hybridization of strains of Salmonella enterica serovar Enteritidis from Uruguay, other distant geographical regions and other serovars isolated in Uruguay

Project description:Microarray based CGH was conducted over a group of 29 strains of S. Enteritidis spanning different epidemiological periods in Uruguay, plus 6 other S. Enteritidis strains isolated from distant geographical regions. We also included 9 Salmonella enterica strains of other serovars isolated in Uruguay. A S. Enteritidis dispensable genome of 233 chromosomal genes and high extent of variation in virulence plasmid was found. Strains isolated before the epidemic show the highest genomic differences as compared with the PT4 reference strain. Comparison with the gene content of other serovars demonstrate extensive horizontal gene transfer between circulating strains beyond serovar definition. Our results show that the epidemic of S Enteritidis in Uruguay was produced by the introduction of strains closely related to PT4, and corroborate the extensive genetic homogeneity among S. Enteritidis isolates worldwide. Phage SE14 emerges as the only specific region for S. Enteritidis. Genetic differences detected in pre-epidemic strains, mainly associated with the absence of phage SE20, suggest that genetic features encoded in this phage may be related to particular epidemiological behavior.

2009-03-03 | E-TABM-603 | biostudies-arrayexpress

Transcription profiling of Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) isolates

Project description:Salmonella enterica serovar Typhimurium (S. Typhimurium) definitive phage type 104 (DT104) has caused significant morbidity and mortality in humans and animals for almost three decades. We have completed the full DNA sequence of one DT104 strain, NCTC13348 and show that the main differences between the genome of this isolate and the previously sequenced S. Typhimurium LT2 lie in integrated prophage elements and the Salmonella Genomic Island 1 encoding antibiotic resistance genes. Thirteen isolates of S. Typhimurium DT104 with different pulsed field gel electrophoresis (PFGE) profiles were analyzed by multi locus sequence typing (MLST), plasmid profiling, hybridization to a Pan-Salmonella DNA microarray and prophage-based multiplex PCR. All the isolates belonged to a single MLST type ST19. Microarray data demonstrated that the 13 DT104 isolates were remarkably conserved in gene content. The PFGE band-size differences in these isolates could be explained to a great extent by changes in prophage and plasmid content. Thus, here the nature of variation in different S. Typhimurium DT104 isolates is further defined at the genome level illustrating how this phage type is evolving over time.

2008-09-05 | E-MTAB-20 | biostudies-arrayexpress

Poly(A) tail length profiling of mRNAs from fission yeast

Project description:To obtain global data on polyadenylation of mRNAs, we fractionated the mRNAs according to their poly(A) tail length using a poly-U sepharose column followed by differential elution at five temperatures. Five mRNA fractions with distinct ranges of poly(A) tail length were then hybridized to microarrays using total eluate as a reference.

2007-05-16 | E-TABM-217 | biostudies-arrayexpress

A coordintate global control over cellular transcription

Project description:Although much is known about the regulation of eukaryotic transcription, the global controls which determine rates of total transcription within a cell are not well understood. We have investigated the effects that the DNA to protein ratio has on both total cellular transcription and the transcription of individual mRNA genes in the unicellular eukaryote fission yeast. Mutants altered in cell size and those blocked in cell cycle progression were used to vary the DNA to protein ratio over a fivefold range around the wild type value. We find that cells of sizes within twofold of wild type value regulate global transcription to maintain similar transcription rates per protein regardless of the cellular DNA content. These changes in total transcription were correlated with coordinated changes in gene occupancy by RNA polymerase II. In large cell cycle arrested mutants, when the DNA to protein ratio falls to a low level, total transcription rates plateau as DNA becomes limiting for transcription1. Unexpectedly, expression levels of individual genes remained tightly coordinated with each other over the entire range of cell sizes. We propose that there is a coordinated, global cellular control which determines the rate of transcription of most genes in the genome and that this control plays a role in regulating the overall growth rate of the cell. Normalized data generated using protocol P-TABM-1335 is available in file ZHURINSKY_NORMALISED_DATA.txt in the additional data archive.

2011-09-23 | E-TABM-1075 | biostudies-arrayexpress

Transcription profiling of fission yeast with deletion or overexpression of ste11 and changes in gene expression after nitrogen starvation of h plus, h minus, h90fus1 and h90ste11 cells to investigate control of gene expression during early sexual differentiation

Project description:Fission yeast cells belong to one of two specialized cell types, M or P. Specific environmental conditions trigger sexual differentiation, which leads to an internal program starting with pheromone signalling between M and P cells, followed by mating, meiosis and sporulation. The initial steps of this process are controlled by Ste11p, a master transcriptional regulator that activates the expression of cell type-specific genes (only expressed in either M or P cells) as well as genes expressed in both M and P cells. <br><br> Pheromone signalling is activated by Ste11p-dependent transcription, and in turn enhances some of this transcription in a positive feedback. To obtain a genome-wide view of Ste11p target genes, their cell-type specificity, and their dependence on pheromone, we used DNA microarrays along with different genetic and environmental manipulations of fission yeast cells.We directly compared the transcriptome of homothallic wild-type cells (h90 fus1) with that of ste11 delta mutants under conditions that induce sexual differentiation. To allow for indirect effects of the ste11 delta mutation, we took advantage of the fact that ectopic expression of ste11 can drive cells into sexual differentiation and therefore is expected to cause the expression of Ste11p targets. We thus defined Ste11p targets as those genes whose expression was significantly reduced in a ste11 delta mutant and significantly increased when ste11 is overexpressed in vegetative cells.<br> <br> This study looked at the effect of deletion or overexpression of ste11, and changes in gene expression after nitrogen starvation of h plus, h minus, h90fus1 and h90ste11 cells.

2006-09-22 | E-TABM-139 | biostudies-arrayexpress

Translation profiling of Schizosaccharomyces pombe size separated polysome fractions provides data on average numbers of associated ribosomes for most transcripts

Project description:To obtain translational profiles for all mRNAs, polysome preparations are separated according to their size using a sucrose gradient and the mRNAs in each fraction are identified and quantified with DNA microarrays. Starting with exponentially growing cells, we analyzed 12 polysome fractions using DNA microarrays containing elements for all known and predicted genes of fission yeast. This approach provided data on average numbers of associated ribosomes for most transcripts.

2007-03-22 | E-TABM-222 | biostudies-arrayexpress

Chromatin immunoprecipitation to measure RNA polymerase II occupancy in fission yeast

Project description:The relative amount of RNA polymerase II (Pol II) associated with a given ORF provides an estimate for transcriptional efficiency. We therefore established a systematic approach to measure Pol II occupancy using chromatin immunoprecipitation followed by analysis on microarrays

2007-03-22 | E-TABM-219 | biostudies-arrayexpress

Transcription profiling of 61 Salmonella enterica serovar Typhimurium isoltates to identify hotspots in genome variation and distinguish between different isolates from the same geographical region

Project description:A collection of 61 Salmonella enterica serovar Typhimurium (S. Typhimurium) of animal and human origin, matched as closely as possible by phage type, antimicrobial resistance pattern and place / time of isolation, and sourced from farms or hospitals in Scotland, were analysed by antimicrobial susceptibility testing, phage typing, pulsed field gel electrophoresis (PFGE), plasmid profiling and DNA microarrays. PFGE of all 61 isolates revealed ten PFGE profiles, which clustered by phage type and antibiotic resistance pattern, with human and animal isolates distributed between PFGE profiles. Analysis of 23 representative S. Typhimurium strains hybridised to a composite Salmonella DNA microarray identified a small number of specific regions of genome variation between different phage types and PFGE profiles. These variable regions of DNA were typically located within prophage-like elements. Simple PCR assays were subsequently designed to discriminate between different isolates from the same geographical region.

2007-06-09 | E-SGRP-6 | biostudies-arrayexpress

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