Transcription profiling of fission yeast wild type and Pab2 knockout strains to invstigate the role of Pab2 in synthesis of noncoding snoRNAs
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ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
SUBMITTER: sanjay khadayate
PROVIDER: E-TABM-843 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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: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-301 | biostudies-arrayexpress
Project description:Small non-coding RNA biogenesis typically involves cleavage of structured precursors by RNase III-like endonucleases. However, guide RNAs that direct U-insertion/deletion mRNA editing in mitochondria of trypanosomes maintain 5â² triphosphate characteristic of transcription start site and possess U-tail indicative of 3â² processing and uridylation. Here, we identified a protein complex composed of RET1 TUTase and 3â²-5â² DSS1 exonuclease, and three additional subunits. This complex, termed mitochondrial 3â² processome (MPsome), is responsible for primary uridylation of ~800-nt gRNA precursors, their processive degradation to a mature length of 50-60 nt, and secondary U-tail addition. Both strands of gRNA gene are transcribed giving rise to sense and antisense precursors of similar size. Head-to-head hybridization of these transcripts blocks symmetrical 3â²-5â² degradation at the fixed distance from the double-stranded region. Together, our findings suggest a model in which gRNA is derived from the 5â² extremity of a primary molecule by uridylation-induced, antisense transcription-controlled exonucleolytic degradation. 1. we first sequenced guide RNA precursor (Gel-fractioned total cellular RNA 600-1500nt was used) transcripts from three replicates to study the their tail features and also validate observation of sense/antisense accumulation upon perturbation of pre-processing complex based on few cases. 2. we then sequenced mitochondrial small RNA and built a reference for small RNAs using our custom algorithm. We then took the mitochondrial small RNA data and uncovered the sense/antisense pair. 3. We then used CLIP-Seq data to investigate in vivo binding sites and, together with RNA IP-Seq data to understand what determine the relative abundance of sense and antisense pair of the duplex. 4. We used sequenced small mitochondrial RNA in different RNAi experiments (For RNAi experiments, 30-70nt RNA fraction was gel-isolated from total cellular RNAs) to understand which protein will affect the Utail length in mature small mitochondrial RNA.
2016-02-08 | E-GEOD-71292 | biostudies-arrayexpress
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
Project description:Myc proteins are essential regulators of animal growth during normal development, and their deregulation is one of the main driving factors of human malignancies. They function as transcription factors that (in vertebrates) control many growth- and proliferation-associated genes, and in some contexts contribute to global gene regulation. We combine ChIPseq and RNAseq approaches in Drosophila tissue culture cells to identify a core set of less than 500 Myc target genes, whose salient function resides in the control of ribosome biogenesis. Amongst these genes we find the non-coding snoRNA genes as a large novel class of Myc targets. All assayed snoRNAs are affected by Myc, and many of them are subject to direct transcriptional activation by Myc, both in Drosophila and in vertebrates. The loss of snoRNAs impairs growth during normal development, whereas their overexpression increases tumor mass in a model for neuronal tumors. This work shows that Myc acts as a master regulator of snoRNP biogenesis. In addition, in combination with recent observations of snoRNA involvement in human cancer, it raises the possibility that Myc’s transforming effects are partially mediated by this class of non-coding transcripts.
2015-04-23 | E-MTAB-3209 | biostudies-arrayexpress
Project description:The aim of the present study was to investigate the response of rapeseed microspore-derived embryos (MDE) to osmotic stress at proteome level. The PEG-induced osmotic stress was studied in cotyledonary MDE of two genotypes: Cadeli (D), and Viking (V), which were previously reported to reveal contrasting leaf proteome responses under drought. 156 representative protein spots – obtained by 2D-DIGE – have been selected for MALDI-TOF/TOF, 63 proteins have been successfully identified and divided into 8 functional groups. Eight selected protein accumulation trends were validated by using qRT-PCR. Biomass accumulation in treated D was significantly higher (3-fold) than in V, so we can claim D as resistant to osmotic stress. Cultivar D displayed resistance strategy thanks to accumulation of proteins in energy metabolism, redox homeostasis, protein destination and signalling functional groups accompanied by high ABA and active cytokinins. In contrast, V protein profile displayed high requirements of energy (ATP) and nutrients with a significant number of stress-related proteins and cell structure changes accompanied by quick down-regulation for active CK content, SA, JA, GA20. MDE proteome profile is discussed together with leaf proteome results from our previous study (Urban et al., 2017, 30:152, J. Proteomics). We propose different mechanisms to cope with osmotic stress in the genotypes studied. This proteomic study is a first step to validate MDE as a suitable model for follow-up research on characterization of new crossings, and can be used for selection of resistant genotypes.
2021-06-14 | PXD024552 | Pride
Project description:Genomes pervasively produce long non-coding RNAs (lncRNAs) of largely unknown functions. Some of these lncRNAs have been implicated in roles related to ageing and associated diseases. Here we characterize aal1 (ageing-associated lncRNA 1) which is induced in non-dividing, ageing cells of fission yeast. Deletion of aal1 shortens the chronological lifespan of non-dividing cells, while ectopic overexpression of aal1 from a plasmid prolongs their lifespan, indicating that this lncRNA acts in trans. We find that aal1 genetically interacts with coding genes functioning in processes related to protein translation, and aal1 overexpression leads to repression of ribosomal protein genes and inhibition of cell growth. The aal1 RNA localizes to the cytoplasm and associates with ribosomes. Notably, aal1 deletion or overexpression is sufficient to increase or decrease the cellular ribosome content, respectively. We identify the mRNA rpl1901, encoding a ribosomal protein, as a binding target of aal1. The expression of rpl1901 is moderately repressed by aal1, and such moderate repression is critical and sufficient to extend the chronological lifespan. Remarkably, expression of the yeast aal1 lncRNA in the fly gut triggers a significant extension of the lifespan in flies. Based on these findings, we propose that the aal1 RNA can reduce the ribosome content by decreasing the levels of the Rpl1901 ribosomal protein, thus attenuating protein translation and promoting longevity. Although the aal1 lncRNA itself is not conserved, its effects in the fly raise the possibility that other organisms feature related mechanisms involving conserved ribosome-associated processes to control ageing.
2024-09-05 | PXD045625 | Pride
Project description:The altitude gradient limits the growth and distribution of alpine plants.Alpine plants have developed strategies to survive the extremely cold conditions prevailing at high altitudes; however, the mechanism underlying the evolution of these strategies remains unknown. The alpine plant Potentilla saundersiana is widespread in the Northwestern Tibetan Plateau. In this study, we conducted a comparative proteomics analysis to investigate the dynamic patterns of protein expression of P. saundersiana located at five different altitudes. We detected and functionally characterized 118 differentially expressed proteins. Our study confirmed that increasing levels of antioxidant proteins, and their respective activities, and accumulation of primary metabolites, such as proline and sugar, confer tolerance to the alpine environment in P. saundersiana. Proteins species associated with the epigenetic regulation of DNA stability and post-translational protein degradation were also involved in this process. Furthermore, our results showed that P. saundersiana modulated the root architecture and leaf phenotype to enhance adaptation to alpine environmental stress through mechanisms that involved hormone synthesis and signal transduction, particularly the cross-talk between auxin and strictosidine. Based on these findings, we conclude that P. saundersiana uses multiple strategies to adapt to the high-altitude environment of the Northwestern Tibetan Plateau.
2022-02-22 | PXD001112 | Pride
Project description:Genome-wide translational profiling of rng3-65 compared to wild type cells. We used sucrose gradients to separate RNAs according to the number of associated ribosomes (a surrogate for translational efficiency). Preparation of the extracts and fractionation was carried out as described in Lackner et al, 2007 (Mol Cell 26(1):145-55). The fractions were pooled into four groups (1 closest to the top, i.e. not associated with ribosomes and 4 closest to the bottom, i.e., associated with polysomes). RNA was extracted from the pools and the corresponding pools from wild type and mutant cells were directly compared using DNA microarrays. Changes in translation are expected to alter the number of ribosomes associated with specific transcripts, and therefore result in a redistribution of the RNAs across the different fractions.
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