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

RNA-seq analysis of the overexpression of the Fil1 transcription factor in S. pombe

ABSTRACT: The Fil1 transcription factor regulates the response to amino acid starvation. Here we analyse the effects of overexpressing the fil1 coding sequence and of its deregulated expression. The following strains were used: 1] Strains expressing the fil1 gene under the control of the thiamine-repressible nmt1 promoter (nmt-fil1) 2] Strains in which 6 uORFs (upstream Open Reading Frames) in the fil1 5'-UTR have been inactivated, leading to deregulated translation of the fil1 mRNA (6uORF_mutant)

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Juan Mata

PROVIDER: E-MTAB-6226 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Phenotypic analysis of the fil1 transcription factor from S. pombe

Project description:RNA-seq of fil1 and wilt type mutants in different conditions

2018-02-01 | E-MTAB-5601 | biostudies-arrayexpress

ChIP-seq analysis of the Fil1 transcription factor from S. pombe.

Project description:Identification of the targets of the Fil1 transcription factor, which is involved in the response to nutrient depletion

2018-02-01 | E-MTAB-5580 | biostudies-arrayexpress

Translation Complex Profiling analysed using sequencing (TCP-seq) applied to fission yeast cells (Schizosaccharomyces pombe)

Project description:Translation complexes are stabilised in vivo using formaldehyde. Cells are lysed, and cell extracts are treated with RNase I to produce protected RNA fragments (FPs or footprints). Extracts are then run through sucrose gradients to separate small ribosomal subunits and full ribosomes. FPs are isolated from each of these fractions and analysed by sequencing. Note this is a modified version of ribo-seq (a.k.a. ribosome profiling)

2022-12-02 | E-MTAB-12264 | biostudies-arrayexpress

Effects of cycloheximide (CHX) on ribosome profiling experiments in Schizosaccharomyces pombe

Project description:CHX is an inhibitor of translation elongation often used in ribosome profiling experiments. There is evidence that CHX treatment of cells may cause artefacts in the distribution of ribosomes on mRNAs. We investigate this possibility in S. pombe by performing ribosome profiling in the presence and absence of this drug.

2017-09-05 | E-MTAB-5794 | biostudies-arrayexpress

Ribosome profiling and parallel RNA-seq of S. pombe cells subject to amino acid starvation

Project description:Study aims at investigating the translational response of S. pombe cells to amino acid starvation

2018-02-01 | E-MTAB-5810 | biostudies-arrayexpress

Analysis of cohesin-dependent gene regulation in fission yeast

Project description:In addition to its well-know function in chromosome segregation, increasing evidence implicates cohesin in the control of gene expression. It has been previously reported that inactivation of the cohesin loader Mis4 in G1-arrested cells leads to the dissociation of cohesin from chromatin. We exploited this experimental situation to ask whether this loss of cohesin would affect gene expression on a genome-wide scale. Three independent inoculates (biological replicates) of cells carrying either the thermosensitive mis4-367 or the wild-type mis4+ allele were grown at permissive temperature of 25C. Cells were G1-arrested by titrating out the Cdc10 transcription factor by overexpression of the C-terminal fragment of its binding partner Res1, and then shifted for 2 hours at 37C. Cells were harvested before and after the temperature shift to proceed to total RNA extraction.

2010-08-12 | E-GEOD-23602 | biostudies-arrayexpress

The 19S proteasome subunit Rpt3 regulates distribution of CENP-A by associating with centromeric chromatin

Project description:CENP-A, a variant of histone H3, is incorporated into centromeric chromatin and plays a role during kinetochore establishment. In fission yeast, the localization of CENP-A is limited to a region spanning 10 to 20 kb of the core domain of the centromere. Here, we report a mutant (rpt3-1) in which this region is expanded to 40 to 70 kb. Likely due to abnormal distribution of CENP-A, this mutant exhibits chromosome instability and enhanced gene silencing. Interestingly, the rpt3+ gene encodes a subunit of the 19S proteasome, which localizes to the nuclear membrane. While Rpt3 associates with centromeric chromatin, the mutant protein has lost this localization. A loss of the cut8+ gene encoding an anchor of the proteasome to the nuclear membrane causes similar phenotypes as observed in the rpt3-1 mutant. Thus, we propose that the proteasome (or its subcomplex) associates with centromeric chromatin and regulates distribution of CENP-A. Chromosomal distributions of differentially expressed centromere protein A in wild-type and a proteasome mutant.

2014-04-07 | E-GEOD-44594 | biostudies-arrayexpress

A histone H3K36 chromatin switch coordinates DNA double-strand break repair pathway choice.

Project description:Wildtype and set2delta strains, with samples taken at t=0 and following 30 minutes treatment with 5 µg/ml bleomycin.

2014-06-09 | E-MTAB-2549 | biostudies-arrayexpress

Meta-stable structural variants alter gene expression and quantitative traits in the fission yeast

Project description:To examine whether naturally occurring duplications are altering gene expression we chose eight pairs of closely related strains (less than 150 SNPS between each pair) that contained at least one unshared duplication and performed pair-wise two-colour microarray analysis.

2017-05-30 | E-MTAB-4019 | biostudies-arrayexpress

wild-type and gaf1 mutant cells treated with Torin1 or with a combination of caffeine/rapamycin

Project description:Target of Rapamycin Complex 1 (TORC1) signaling promotes growth and ageing. Inhibition of TORC1 leads to a down-regulation of factors that stimulate protein translation, which in turn contributes to longevity. TORC1-dependent post-transcriptional regulation of protein translation has been well studied, while analogous transcriptional regulation is less understood. Here we screened fission yeast deletion mutants for resistance to Torin1, which inhibits TORC1 and cell growth. Cells lacking the GATA transcription factor Gaf1 (gaf1Δ) grew normally even in high doses of Torin1. The gaf1Δ mutation shortened the chronological lifespan of non-dividing cells and diminished the longevity triggered by Torin1 treatment. Expression profiling and genome-wide binding experiments showed that, upon TORC1 inhibition, Gaf1 directly up-regulated genes for small-molecule metabolic pathways and indirectly repressed genes for protein translation. Surprisingly, Gaf1 bound to, and down-regulated the tRNA genes, so also functions as a transcription factor for genes transcribed by RNA polymerase III. Thus, Gaf1 controls the transcription of both coding and tRNA genes to inhibit translation and growth downstream of TORC1.

2020-03-02 | E-MTAB-8569 | 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