Pombe_ribosome_profiling_pat1_meiotic_cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Schizosaccharomyces pombe
SUBMITTER: Juan Mata
PROVIDER: E-MTAB-2265 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We applied in parallel RNA-Seq and Ribosome-profiling to S. pombe pat1 diploids undergoing meiosis and sporulation in a synchronous manner
2014-06-03 | E-MTAB-2179 | biostudies-arrayexpress
Project description:Changes in gene expression are hallmarks of cellular differentiation. Sexual differentiation in fission yeast (Schizosaccharomyces pombe) provides a model system for gene expression programs accompanying and driving cellular specialization. The expression of hundreds of genes is modulated in successive waves during meiosis and sporulation in S. pombe, and several known transcription factors are critical for these processes. We used DNA microarrays to investigate meiotic gene regulation by examining transcriptomes after genetic perturbations (gene deletion and/or overexpression) of rep1, mei4, atf21 and atf31, which encode known transcription factors controlling sexual differentiation. This analysis reveals target genes at a genome-wide scale and uncovers combinatorial control by Atf21p and Atf31p. We also studied two transcription factors that are upregulated during meiosis but had not been previously implicated in sexual differentiation : Rsv2p induces stress-related genes during spore formation, while Rsv1p acts as a repressor for glucose-metabolism genes. Our data further reveal negative feedback interactions: both Rep1p and Mei4p not only activate specific gene expression waves (early and middle genes, respectively), but are also required for repression of genes induced in the previous waves (Ste11p-dependent and early genes, respectively).
2008-01-01 | E-TABM-300 | biostudies-arrayexpress
Project description:Changes in gene expression are hallmarks of cellular differentiation. Sexual differentiation in fission yeast (Schizosaccharomyces pombe) provides a model system for gene expression programs accompanying and driving cellular specialization. The expression of hundreds of genes is modulated in successive waves during meiosis and sporulation in S. pombe, and several known transcription factors are critical for these processes. We used DNA microarrays to investigate meiotic gene regulation by examining transcriptomes after genetic perturbations (gene deletion and/or overexpression) of rep1, mei4, atf21 and atf31, which encode known transcription factors controlling sexual differentiation. This analysis reveals target genes at a genome-wide scale and uncovers combinatorial control by Atf21p and Atf31p. We also studied two transcription factors that are upregulated during meiosis but had not been previously implicated in sexual differentiation : Rsv2p induces stress-related genes during spore formation, while Rsv1p acts as a repressor for glucose-metabolism genes. Our data further reveal negative feedback interactions: both Rep1p and Mei4p not only activate specific gene expression waves (early and middle genes, respectively), but are also required for repression of genes induced in the previous waves (Ste11p-dependent and early genes, respectively).
2008-01-01 | E-TABM-298 | biostudies-arrayexpress
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
Project description:RNA-Seq from vegetatively growing S. pombe cells carrying mutation in RNA-binding protein genes
2014-12-01 | E-MTAB-2695 | biostudies-arrayexpress
Project description:Progression through meiosis in Schizosaccharomyces pombe is regulated by stage-specific gene expression and translation, changes in RNA stability, expression of anti-sense transcripts and also requires stage-specific, targetted proteolysis of regulatory proteins. We have used SILAC labelling to examine the relative levels of proteins in S. pombe as diploid cells undergo meiosis. We found that the relative level of 880 proteins changes at least two-fold at some stage of meiosis. Most of these proteins either increase or decrease in level during the meiotic divisions, while some show transient peaks of expression. The most notable changes are in the proteostasis network, which shows a significant increase in components involved in protein turnover concomitant to a decrease in proteins involved in ribosome biogenesis. There was also an increase in ESCRT III protein levels; biological analysis reveals a role for some ESCRT III components in chromosome segregation and spore formation. Correlation with previous studies of gene expression and ribosome occupancy through meiosis reveals that changes in steady state protein levels are mainly regulated post-transcriptionally.
2019-02-15 | PXD010438 | Pride
Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using the RNA-binding protein Meu5 from the fission Schizosaccaromyces pombe
2011-01-01 | E-TABM-932 | biostudies-arrayexpress
Project description:Meiotic chromosome architecture called M-bM-^@M-^\axis-loop structuresM-bM-^@M-^] and histone modifications have been demonstrated to regulate the Spo11-dependent formation of DNA double-strand breaks (DSBs) that trigger meiotic recombination. Using genome-wide chromatin immunoprecipitation (ChIP) analyses followed by deep sequencing, we compared the genome-wide distribution of the axis protein Rec8 (the kleisin subunit of meiotic cohesin) with that of oligomeric DNA covalently bound to Spo11, indicative of DSB sites. The frequency of DSB sites is overall constant between Rec8 binding sites. However, DSB cold spots are observed in regions spanning M-BM-10.8 kb around Rec8 binding sites. The axis-associated cold spots are not due to exclusion of Spo11 localization from the axis, since ChIP experiments revealed that substantial Spo11 persists at Rec8 binding sites during DSB formation. Spo11 fused with Gal4 DNA binding domain (Gal4BD-Spo11) tethered in close proximity (M-bM-^IM-$0.8 kb) to Rec8 binding sites hardly forms meiotic DSBs, in contrast with other regions. In addition, H3K4 tri-methylation (H3K4me3) remarkably decreases at Rec8 binding sites. These results suggest that reduced histone H3K4me3 in combination with inactivation of Spo11 activity on the axis discourages DSB hot spot formation. ChIP-chip analysis of Rec8 on fission yeast meiotic chromosomes
2014-03-31 | E-GEOD-52858 | biostudies-arrayexpress
Project description:We applied in parallel RNA-Seq and Ribosome-profiling to vegetatively growing S. pombe cells. Two independent biological repeats were performed.
2014-06-03 | E-MTAB-2176 | biostudies-arrayexpress
Project description:Higher-order chromosome structure is assumed to control various DNA-templated reactions in eukaryotes. Meiotic chromosomes implement developed structures called M-bM-^@M-^\axesM-bM-^@M-^] and M-bM-^@M-^\loopsM-bM-^@M-^]; both are suggested to tether each other, activating Spo11 to catalyze meiotic DNA double-strand breaks (DSBs) at recombination hotspots. We found that the Schizosaccharomyces pombe Spo11 homolog Rec12 and its partners form two distinct subcomplexes, DSBC (Rec6-Rec12-Rec14) and SFT (Rec7-Rec15-Rec24). Additionally, Mde2, whose expression is strictly regulated by the replication checkpoint, interacts with a component of each subcomplex. The SFT subcomplex binds to both axes via direct interaction of Rec15 with Rec10 in axes and DSB sites, hence axial Rec10 can partially tether DSB sites located in loops. Importantly, this multiprotein-based tethered axis-loop complex is destabilized in the absence of Mde2. We therefore propose a novel mechanism by which Mde2 functions as a recombination initiation mediator to tether axes and loops, in liaison with the meiotic replication checkpoint. ChIP-chip analyses of Rec10 (in wild type), Mde2 (in wild type and rec15M-bM-^HM-^F), and Rec15 (in wild type, rec10M-bM-^HM-^F, rec24M-bM-^HM-^F and mde2M-bM-^HM-^F) at meiosis 4 hours.
2012-07-27 | E-GEOD-31846 | biostudies-arrayexpress