Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-22809
PROVIDER: PRJNA127897 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:During meiotic prophase, concurrent transcription, recombination, and chromosome synapsis place substantial topological strain on chromosomal DNA, but the role of topoisomerases in this context remains poorly defined. Here, we analyzed the roles topoisomerases I and II (Top1 and Top2) during meiotic prophase in Saccharomyces cerevisiae. We show that both topoisomerases accumulate primarily in promoter-containing intergenic regions of actively transcribing genes, including many meiotic double-strand break (DSB) hotspots. Despite the comparable binding patterns, top1 and top2 mutations have different effects on meiotic recombination. TOP1 disruption delays DSB induction and shortens the window of DSB accumulation by an unknown mechanism. By contrast, temperature-sensitive top2-1 mutants exhibit a marked delay in meiotic chromosome remodeling and elevated DSB signals on synapsed chromosomes. The problems in chromosome remodeling were linked to altered Top2 binding patterns rather than a loss of Top2 catalytic activity and stemmed from a defect in recruiting the chromosome remodeler Pch2/TRIP13 to synapsed chromosomes. No chromosomal defects were observed in the absence of TOP1. Our results imply independent roles for topoisomerases I and II in modulating meiotic chromosome structure and recombination.
2020-03-06 | GSE131994 | GEO
Project description:Topoisomerase II binds nucleosome-free DNA and acts redundantly with Topoisomerase I to enhance recruitment of RNA Pol II in budding yeast
| PRJNA128205 | ENA
Project description:Here we dissect the transcriptional response in S. cerevisiae cells lacking DNA topoisomerases. We use microarray technology coupled with a functional genomics approach and demonstrate intimate connections between topoisomerase dependency, promoter chromatin architecture and gene transcription. Our findings suggest that DNA topoisomerases I and II play a role for transcription initiation. We observe a genome wide reduction in mRNA levels and identify a distinct functional subset of the genome with particular requirements for topoisomerases. These genes are characterized by high transcriptional plasticity, they are chromatin regulated and distinguished by having an enrichment of a nucleosome at a critical position in the promoter region, suggesting that topoisomerases influence transcription initiation by affecting promoter chromatin structure. In further support of a role of topoisomerases for initiation, we demonstrate that genome wide topoisomerase dependency reflects transcriptional activity but not transcriptional length. We exemplify the importance of topoisomerases for initiation of chromatin-regulated genes by showing that the enzymes are essential although redundant for PHO5 induction and are necessary for a step required for promoter nucleosome removal. W303 versus top1Î?, top2ts and top1Î?top2ts. 3 biological replicates for each mutant versus wildtype counterpart amounting to 12 microarrays.
2012-07-31 | E-GEOD-22809 | biostudies-arrayexpress
Project description:Transcription has the capacity to modify mechanically DNA topology, DNA structure, and nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn, may provide instant feedback to the transcription machinery. To substantiate the connection between transcription and DNA dynamics, we charted an ENCODE map of transcription-dependent dynamic supercoiling in human Burkitt lymphoma cells using psoralen photobinding to probe DNA topology in vivo. Dynamic supercoils spread ~1.5 kb upstream of the start sites of active genes. Low and high output promoters handle this torsional stress differently as shown using inhibitors of transcription and topoisomerases, and by chromatin immunoprecipation of RNA polymerase and topoisomerases I and II. Whereas lower outputs are managed adequately by topoisomerase I, high output promoters additionally require topoisomerase II. The genome-wide coupling between transcription and DNA topology emphasizes the importance of dynamic supercoiling for gene regulation.
2013-02-16 | GSE43751 | GEO
Project description:Eukaryotic topoisomerase I and II relax DNA and are key components in the processes of DNA replication, transcription and genome stability. It is not clear, however, how their activity controls epigenetic states across an entire eukaryotic genome. Using the fission yeast model Schizosaccharomyces pombe, we investigate genome-wide how topoisomerases affect chromatin formation through nucleosome occupancy and regulate transcription. We show that topoisomerase activity is required for nucleosome turnover at promoter regions, affecting epigenetic gene regulatory states, and for effective termination of transcription.
2010-07-02 | E-MEXP-1850 | biostudies-arrayexpress
Project description:Transcription has the capacity to modify mechanically DNA topology, DNA structure, and nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn, may provide instant feedback to the transcription machinery. To substantiate the connection between transcription and DNA dynamics, we charted an ENCODE map of transcription-dependent dynamic supercoiling in human Burkitt lymphoma cells using psoralen photobinding to probe DNA topology in vivo. Dynamic supercoils spread ~1.5 kb upstream of the start sites of active genes. Low and high output promoters handle this torsional stress differently as shown using inhibitors of transcription and topoisomerases, and by chromatin immunoprecipation of RNA polymerase and topoisomerases I and II. Whereas lower outputs are managed adequately by topoisomerase I, high output promoters additionally require topoisomerase II. The genome-wide coupling between transcription and DNA topology emphasizes the importance of dynamic supercoiling for gene regulation. Raji cells: untreated and treated with DRB, CPT and BLAP. Three biological replicates per treatment, each hybridized to new array. Total: 12 samples (4 treatments x 3 replicates).
2013-02-16 | E-GEOD-43751 | biostudies-arrayexpress
Project description:DNA topoisomerases are known to promote transcription in prokaryotes by removing excessive DNA supercoils produced during elongation. However, it is unclear how topoisomerases in eukaryotes are recruited and function in the transcription pathway in the context of nucleosomes. To address this problem we present high-resolution genome wide maps of one of the major eukaryotic topoisomerases, Topoisomerase II (Top2) and nucleosomes in the budding yeast, Saccharomyces cerevisiae. Our data indicate that at promoters Top2 binds primarily to DNA that is nucleosome free. However, while nucleosome loss enables Top2 occupancy the opposite is not the case and the loss of Top2 has little effect on nucleosome density. We also find that Top2 is involved in transcription. Not only is Top2 enriched at highly transcribed genes but Top2 is required redundantly with Top1 for optimal recruitment of RNA polymerase II at their promoters. These findings and the examination of candidate activated genes suggest that nucleosome loss induced by nucleosome remodeling factors during gene activation enable Top2 binding which in turn acts redundantly with Top1 to enhance recruitment of RNA polymerase II.
2011-08-01 | GSE22626 | GEO
Project description:DNA topoisomerase 3A (TOP3A) and mitochondrial DNA topoisomerase 1 (TOP1MT) play an important role in the maintenance and topological control of the mitochondrial DNA. In this study TOP3A, TOP1MT or both TOP3A and TOP1MT have been knocked down using siRNAs to determine the effect of the topoisomerases on mitochondrial transcription. RNA was isolated from ctrl siRNA, TOP3A siRNA, TOP1MT siRNA and TOP3A + TOP1MT siRNA transfected cells after 6 days of transfection.
2022-10-11 | GSE201426 | GEO
Project description:Topoisomerases are necessary for the expression of neurodevelopmental genes, and are mutated in some patients with autism spectrum disorder (ASD). We have studied the effects of inhibitors of Topoisomerase 1 (Top1) and Topoisomerase 2 (Top2) enzymes on mouse cortical neurons. We find that topoisomerases selectively inhibit long genes (>100kb), with little effect on all other gene expression. Using ChIPseq against RNA Polymerase II (Pol2) we show that the Top1 inhibitor topotecan blocks transcriptional elongation of long genes specifically. Many of the genes inhibited by topotecan are candidate ASD genes, leading us to propose that topoisomerase inhibition might contribute to ASD pathology.
2013-08-30 | GSE43526 | GEO
Project description:Topoisomerases are necessary for the expression of neurodevelopmental genes, and are mutated in some patients with autism spectrum disorder (ASD). We have studied the effects of inhibitors of Topoisomerase 1 (Top1) and Topoisomerase 2 (Top2) enzymes on mouse cortical neurons. We find that topoisomerases selectively inhibit long genes (>100kb), with little effect on all other gene expression. Using ChIPseq against RNA Polymerase II (Pol2) we show that the Top1 inhibitor topotecan blocks transcriptional elongation of long genes specifically. Many of the genes inhibited by topotecan are candidate ASD genes, leading us to propose that topoisomerase inhibition might contribute to ASD pathology.
2013-08-30 | GSE43899 | GEO