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PROVIDER: PRJNA227342 | ENA |
REPOSITORIES: ENA
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Project description:Global analyses of cell cycle dependent changes in fission yeast genome organization reveal correlations with alterations in transcript levels [GCC]
| PRJNA227346 | ENA
Project description:Global analyses of cell cycle dependent changes in fission yeast genome organization reveal correlations with alterations in transcript levels [RNA-Seq]
| PRJNA227345 | ENA
Project description:The successful progression of a cell through the cell cycle requires the temporal regulation of many biological processes, including gene transcript levels and the number and condensation of chromosomes. Fission yeast (Schizosaccharomyces pombe) is a paradigm for cell cycle research and model for higher eukaryotic cells. Due to the small size of its genome, it is highly amenable to high resolution studies of the spatial organization of its genome. Here we present the results of a high resolution study in which we used synchronised S. pombe cells to investigate cell cycle phase dependent changes in genome organization and transcription patterns. We reveal cell cycle dependant changes in connections within and between chromosomes while confirming previously observed features of genome organization, such as telomere clustering. Our results show that chromosomes are effectively circular throughout the cell cycle and that they remain connected even during the M phase. Determining the structure and transcript levels for matched synchronized cells revealed: 1) that genes with high transcript levels are highly connected with the genome at specific stages of the cell cycle; and 2) that interactions have positive and negative effects on transcript levels. We hypothesize that the observed correlations between transcript levels and the formation and disruption of cell cycle specific chromosomal interactions implicate genome organization in epigenetic inheritance and bookmarking.
2014-11-07 | GSE52284 | GEO
Project description:The successful progression of a cell through the cell cycle requires the temporal regulation of many biological processes, including gene transcript levels and the number and condensation of chromosomes. Fission yeast (Schizosaccharomyces pombe) is a paradigm for cell cycle research and model for higher eukaryotic cells. Due to the small size of its genome, it is highly amenable to high resolution studies of the spatial organization of its genome. Here we present the results of a high resolution study in which we used synchronised S. pombe cells to investigate cell cycle phase dependent changes in genome organization and transcription patterns. We reveal cell cycle dependant changes in connections within and between chromosomes while confirming previously observed features of genome organization, such as telomere clustering. Our results show that chromosomes are effectively circular throughout the cell cycle and that they remain connected even during the M phase. Determining the structure and transcript levels for matched synchronized cells revealed: 1) that genes with high transcript levels are highly connected with the genome at specific stages of the cell cycle; and 2) that interactions have positive and negative effects on transcript levels. We hypothesize that the observed correlations between transcript levels and the formation and disruption of cell cycle specific chromosomal interactions implicate genome organization in epigenetic inheritance and bookmarking.
2014-11-07 | GSE52283 | GEO
Project description:This project aims to identify molecular effects of loss of individual SHREC components on fission yeast transcriptional program RNA-seq was utilized to compare transcript levels between wild type, clr1D, clr2D, clr3D, mit1D and chp2D fission yeast
2016-05-06 | GSE73359 | GEO
Project description:Architectural alterations of the fission yeast genome across the cell cycle
| PRJNA360306 | ENA
Project description:ChIP-chip analyses of Psc3 in wild-type and mutant fission yeast cells. Eukaryotic genomes are folded into three-dimensional structures that govern diverse hromosomal procsses. Studeis in Drosophila and mammals have revealed large self-associating tomological domains whose borders are enriched in cohesin/CTCF factors that are required for long-range intrations. However, mechanisms governing higher-order folding of chromatin fivbers and the exact function of cohesin in this process remain poor understood. Here we perform Hi-C to explore the organization of the Schizosaccharomyces pombe genome at high-resolution, which despite its small size comprises fundamental features found in higher eukaryotes. Our analyses reveal that in addition to determinants of Rabl-like chromosome architecture, smaller locally interacting regions of chromatin, referred to as globules, are a distinctive features of S. pombe chromosome organization. This feature of chromatin architecture requires a function of cohesin distinct from its role in sister chromatid cohesion. Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structure and global chromosome territories. Heterochromatin, which selectively loads cohesin at specific loci including pericentromric and subtelomeric domains, is dispensable for globule formation but uniquely impacts genome organization through chromatin compaction by enforcing Rabl configuration. Genome-wide distribution of Psc3 were determined by ChIP-chip analysis in wild-type and mutant fission yeast cells.
2014-10-22 | E-GEOD-56848 | biostudies-arrayexpress
Project description:Aims: To map histone modifications with unprecedented resolution both globally and locus-specifically, and to link modification patterns to gene expression. Materials & methods: Using correlations between quantitative mass spectrometry and chromatin immunoprecipitation/microarray analyses, we have mapped histone post-translational modifications in fission yeast (Schizosaccharomyces pombe). Results: Acetylations at lysine 9, 18 and 27 of histone H3 give the best positive correlations with gene expression in this organism. Using clustering analysis and gene ontology search tools, we identified promoter histone modification patterns that characterize several classes of gene function. For example, gene promoters of genes involved in cytokinesis have high H3K36me2 and low H3K4me2, whereas the converse pattern is found ar promoters of gene involved in positive regulation of the cell cycle. We detected acetylation of H4 preferentially at lysine 16 followed by lysine 12, 8 and 5. Our analysis shows that this H4 acetylation bias in the coding regions is dependent upon gene length and linked to gene expression. Our analysis also reveals a role for H3K36 methylation at gene promoters where it functions in a crosstalk between the histone methyltransferase Set2KMT3 and the histone deacetylase Clr6, which removes H3K27ac leading to repression of transcription. Conclusion: Histone modification patterns could be linked to gene expression in fission yeast.
2011-01-05 | GSE11511 | GEO
Project description:The expression of a large proportion of the fission yeast genome changes periodically with the cell cycle. Several key transcription factors have been identified that regulate these oscillating and interdependent waves of gene expression. However, for a significant number of cell cycle-regulated genes the regulator(s) driving these oscillations remain unknown. Cbf11 and Cbf12, the fission yeast CSL transcription factors, have been implicated in the regulation of cell cycle progression, yet the details of their functioning are poorly understood. Using a combination of transcriptome profiling and genome-wide mapping of CSL-DNA interactions we have identified a comprehensive set of CSL-regulated genes. Our data indicate that Cbf11 and Cbf12 contribute directly and indirectly to the regulation of periodically expressed genes in fission yeast. We show that during S phase/cytokinesis Cbf11 directly activates the transcription of several periodic genes required in the cell to prevent catastrophic mitosis. In agreement with these findings, multiple aspects of cell cycle progression are perturbed when CSL cellular levels are genetically manipulated. We have identified Cbf11 as a novel cell cycle phase-specific activator of genes required for proper coordination of cell and nuclear division, and prevention of catastrophic mitosis in fission yeast.
2015-09-18 | E-MTAB-2724 | biostudies-arrayexpress
Project description:The expression of a large proportion of the fission yeast genome changes periodically with the cell cycle. Several key transcription factors have been identified that regulate these oscillating and interdependent waves of gene expression. However, for a significant number of cell cycle-regulated genes the regulator(s) driving these oscillations remain unknown. Cbf11 and Cbf12, the fission yeast CSL transcription factors, have been implicated in the regulation of cell cycle progression, yet the details of their functioning are poorly understood. Using a combination of transcriptome profiling and genome-wide mapping of CSL-DNA interactions we have identified a comprehensive set of CSL-regulated genes. Our data indicate that Cbf11 and Cbf12 contribute directly and indirectly to the regulation of periodically expressed genes in fission yeast. We show that during S phase/cytokinesis Cbf11 directly activates the transcription of several periodic genes required in the cell to prevent catastrophic mitosis. In agreement with these findings, multiple aspects of cell cycle progression are perturbed when CSL cellular levels are genetically manipulated. We have identified Cbf11 as a novel cell cycle phase-specific activator of genes required for proper coordination of cell and nuclear division, and prevention of catastrophic mitosis in fission yeast.
2015-09-18 | E-MTAB-2725 | biostudies-arrayexpress