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

High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture [Expression Array]

Project description: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. Agilent 60mer oligonucleotide custom array containing probes spanning large portion of chromosome 2 at 50bp resolution was used to profile expression levels in mutant cells and to compare them to levels in wild type cells.

2014-10-22 | E-GEOD-57159 | biostudies-arrayexpress

Mapping of Rec12 oligonucleotides in Schizosaccharomyces pombe

Project description:Meiotic recombination facilitates accurate pairing and faithful segregation of homologous chromosomes by forming physical connections (crossovers) between homologs. Developmentally programmed DNA double-strand breaks (DSBs) generated by Spo11 protein (Rec12 in fission yeast) initiate meiotic recombination. Until recently, attempts to address the basis of the highly non-random distribution of DSBs on a genome-wide scale have been limited to 0.1–1 kb resolution of DSB position. We have assessed individual DSB events across the Schizosaccharomyces pombe genome at near-nucleotide resolution by deep-sequencing the short oligonucleotides connected to Rec12 following DNA cleavage. The single oligonucleotide size-class generated by Rec12 allowed us to effectively analyze all break events. Our high-resolution DSB map shows that the influence of underlying nucleotide sequence and chromosomal architecture differs in multiple ways from that in budding yeast. Rec12 action is not strongly restricted to nucleosome-depleted regions but is nevertheless spatially biased with respect to chromatin structure. Furthermore, we find strong evidence across the genome for differential DSB repair previously predicted to account for crossover invariance (constant cM/kb in spite of DSB hotspots). Our genome-wide analyses demonstrate evolutionarily fluid factors contributing to crossover initiation and its regulation.

2014-06-25 | GSE49977 | GEO

High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture [microarray CGH]

Project description: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. microarray CGH analysis in mutant fission yeast cell; Copy number change in rad21-K1 were examined by comparative genomic hybridization analysis.

2014-10-22 | E-GEOD-56847 | biostudies-arrayexpress

Schizosaccharomyces pombe

Project description:ChIP-chip analyses of SWIRM1 and SWIRM2 across the S. pombe genome.

| PRJNA99081 | ENA