High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture
Ontology highlight
ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
PROVIDER: GSE56849 | GEO | 2014/10/22
SECONDARY ACCESSION(S): PRJNA244762
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-10-22 | E-GEOD-56849 | biostudies-arrayexpress
Project description:Eukaryotic genomes are folded into a hierarchy of three-dimensional structures that impact nuclear functions, including transcription, replication, and repair1-3. Studies in Drosophila and mammals have revealed megabase-sized topologically associated domains (TADs) within chromosomes, which in turn are spatially restricted within the nucleus4-8. However, little is known about local physical constraints that drive higher-order folding of chromosomes. Here we performed Hi-C analysis of the fission yeast Schizosaccharomyces pombe to explore genome organization at high resolution. S. pombe comprises a small genome ideal for examining structural features of chromatin folding, and contains fundamental components present in higher eukaryotes. Large domains of heterochromatin coat centromeres and telomeres and recruit cohesin, a ring-like protein complex that binds sister chromatids and mediates long range looping of interphase chromosomes. Our analyses reveal a highly ordered chromosome organization, consistent with a Rabl configuration, which is dependent on constraints imposed at centromeres and telomeres. We find that local chromatin compaction and cohesin recruitment to centromeres mediated by heterochromatin is required for maintaining global genome territorial restraint. In addition to larger complex domains, we also observed locally interacting regions of chromatin ~50 kilobases long, which organize chromosome arms into structures referred to as “globules”. Globule boundaries are enriched in cohesin and convergent gene orientation. The role of cohesin in maintaining globule domains is independent of its role in sister chromatid cohesion, as globule domains are also a feature of G1 chromosome architecture. Defect in cohesin disrupts globule domains and results in an altered chromosome organization at larger scales, including the loss of chromosome territories. Disruption of globules also affects functional annotation of the genome, leading to impairment of borders between neighboring transcriptional units. Our analyses reveal key features of chromatin organization and folding and show that distinct mechanisms uniquely impact the hierarchy of genome organization to protect genome integrity and to coordinate nuclear functions. Comparison of HiC contact maps under various conditions reveal fundamental principles of genome organization
2014-10-22 | E-GEOD-57316 | biostudies-arrayexpress
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: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
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
Project description:Eukaryotic genomes are folded into a hierarchy of three-dimensional structures that impact nuclear functions, including transcription, replication, and repair1-3. Studies in Drosophila and mammals have revealed megabase-sized topologically associated domains (TADs) within chromosomes, which in turn are spatially restricted within the nucleus4-8. However, little is known about local physical constraints that drive higher-order folding of chromosomes. Here we performed Hi-C analysis of the fission yeast Schizosaccharomyces pombe to explore genome organization at high resolution. S. pombe comprises a small genome ideal for examining structural features of chromatin folding, and contains fundamental components present in higher eukaryotes. Large domains of heterochromatin coat centromeres and telomeres and recruit cohesin, a ring-like protein complex that binds sister chromatids and mediates long range looping of interphase chromosomes. Our analyses reveal a highly ordered chromosome organization, consistent with a Rabl configuration, which is dependent on constraints imposed at centromeres and telomeres. We find that local chromatin compaction and cohesin recruitment to centromeres mediated by heterochromatin is required for maintaining global genome territorial restraint. In addition to larger complex domains, we also observed locally interacting regions of chromatin ~50 kilobases long, which organize chromosome arms into structures referred to as “globules”. Globule boundaries are enriched in cohesin and convergent gene orientation. The role of cohesin in maintaining globule domains is independent of its role in sister chromatid cohesion, as globule domains are also a feature of G1 chromosome architecture. Defect in cohesin disrupts globule domains and results in an altered chromosome organization at larger scales, including the loss of chromosome territories. Disruption of globules also affects functional annotation of the genome, leading to impairment of borders between neighboring transcriptional units. Our analyses reveal key features of chromatin organization and folding and show that distinct mechanisms uniquely impact the hierarchy of genome organization to protect genome integrity and to coordinate nuclear functions.
2014-10-22 | GSE57316 | GEO
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.
2014-10-22 | GSE56847 | GEO
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.
2014-10-22 | GSE57159 | GEO
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.
2014-10-22 | GSE56848 | GEO
Project description:High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture
| PRJNA244762 | ENA