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Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast

ABSTRACT: Characterize the transcriptional response to INO2 and INO4 expression level (INO-level) and efficient factor

ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe

PROVIDER: GSE36298 | GEO | 2013/12/23

SECONDARY ACCESSION(S): PRJNA153037

REPOSITORIES: GEO

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Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast

Project description:Characterize the transcriptional response to INO2 and INO4 expression level (INO-level) and efficient factor We used microarrays to capture the global responses of INO-level in Carbon and Nitrogen limited growth.

2013-12-23 | E-GEOD-36298 | biostudies-arrayexpress

Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast.

Project description: Not available

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Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion

Project description:We performed whole genome analysis of the DNA binding of five Saccharomyces cerevisiae transcription factors involved in lipid biosynthesis, Ino2, Ino4, Hap1, Oaf1 and Pip2, in response to four different environmental conditions. Using chromatin immunoprecipitation with lambda exonuclease digestion (ChIP-exo) we discovered a large number of so-far unidentified targets with nucleotide resolution. Based on the newly identified targets we document expanded functions for all five transcription factors, e.g. glutamate biosynthesis as a target of Oaf1 and Pip2. Moreover, condition-dependent binding of transcription factors in response to cell metabolic state, e.g. differential binding of Ino2 between fermentative and respiratory metabolic conditions was clearly suggested. Using our data we build a comprehensive transcriptional regulatory network for lipid metabolism in yeast.

2018-07-05 | GSE88941 | GEO

Saccharomyces cerevisiae

Project description:Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast

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Bas1 and Ino4 ChIP-seq

Project description:Meiotic recombination is initiated by developmentally programmed DNA double-strand breaks (DSBs). In S. cerevisiae, the vast majority of DSBs occur in the nucleosome-depleted regions at gene promoters, where transcription factors (TFs) bind. It has been proposed that TF binding can stimulate DSB formation nearby by modulating local chromatin structure. However, a prior study in TF bas1 mutant suggested that the role of TF binding in determining break formation is complex. Here, we examined fine-scale DSB distributions in TF mutant (bas1Δ and ino4Δ) strains. In bas1Δ mutants, 239 out of the 2468 hotspots showed reduced DSB activity, whereas 87 hotspots showed increased DSB activity. Similarly, in ino4Δ mutant, 415 out of the 2468 hotspots showed reduced DSB activity, whereas 322 hotspots showed increased DSB activity. We also mapped Bas1 and Ino4 binding sites in meiosis and found that only a small portion of the affected hotspots contained TF binding sites. This indicates that TF can influence DSB distribution both directly and indirectly. Surprisingly, these DSB changes in TF mutants did not correlate with change in chromatin structure and histone H3K4me3 modification, suggesting that the role of TF on DSB distribution cannot be simply explained by affecting local chromatin status. Four samples total: Bas1-Myc (ChIP and input samples), Ino4-Myc (ChIP and input samples)

2015-08-21 | E-GEOD-67912 | biostudies-arrayexpress

Spo11-oligo mapping in bas1 and ino4 mutants

Project description:Meiotic recombination is initiated by developmentally programmed DNA double-strand breaks (DSBs). In S. cerevisiae, the vast majority of DSBs occur in the nucleosome-depleted regions at gene promoters, where transcription factors (TFs) bind. It has been proposed that TF binding can stimulate DSB formation nearby by modulating local chromatin structure. However, a prior study in TF bas1 mutant suggested that the role of TF binding in determining break formation is complex. Here, we examined fine-scale DSB distributions in TF mutant (bas1Δ and ino4Δ) strains. In bas1Δ mutants, 239 out of the 2468 hotspots showed reduced DSB activity, whereas 87 hotspots showed increased DSB activity. Similarly, in ino4Δ mutant, 415 out of the 2468 hotspots showed reduced DSB activity, whereas 322 hotspots showed increased DSB activity. We also mapped Bas1 and Ino4 binding sites in meiosis and found that only a small portion of the affected hotspots contained TF binding sites. This indicates that TF can influence DSB distribution both directly and indirectly. Surprisingly, these DSB changes in TF mutants did not correlate with change in chromatin structure and histone H3K4me3 modification, suggesting that the role of TF on DSB distribution cannot be simply explained by affecting local chromatin status. Nine samples total: two wild type, four bas1 mutant and three ino4 mutant (each an independent culture)

2015-08-21 | E-GEOD-67910 | biostudies-arrayexpress

Reprogrammed lipid metabolism protects inner nuclear membrane against unsaturated fat

Project description:Transcriptome analysis of ino4∆ and Mga2∆TM-overexpressing cells in order to understand the mechanism by which cells decide whether to synthesize LDs from the INM or not. A striking difference between the transcriptomes of Mga2∆TM-overexpressing cells (cLDs) and ino4∆ cells (cLDs and nLDs) is the fact that enzymes involved in PL synthesis, for example, the phosphatidylethanolamine methyltransferase CHO2 or the phospholipid methyltransferase OPI3, are downregulated specifically in ino4∆ cells. In contrast, Mga2∆TM overexpressing cells showed an upregulation of the Ole1 desaturase and Mvd1, an enzyme involved in sterol biosynthesis, whereas the expression of PL synthesis factors remained largely unchanged.

2021-08-17 | GSE156951 | GEO

Expression analysis with Phospholipase C over expression

Project description:The regulation of phospholipid biosynthesis in Saccharomyces cerevisiae through cis-acting upstream activating sequence inositol (UASino) and trans-acting elements, such as the INO2-INO4 complex and OPI1 by inositol supplementation in growth is thoroughly studied. In this study, we provide evidence for the regulation of lipid biosynthesis by phosphatidylinositol-specific phospholipase C (PLC) through UASino and two trans-acting elements. Gene expression analysis and radiolabelling experiments demonstrated that the overexpression of rice PLC in yeast cells altered phospholipid biosynthesis at the levels of transcriptional and enzyme activity.

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Expression analysis with Phospholipase C over expression

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Lipidome and proteome of lipid droplets from the methylotrophic yeast Pichia pastoris.

Project description: Not available

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