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Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [Mnase-seq]

ABSTRACT: Investigate the role of topoisomerase 1 in the response to oxidative stress

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE227182 | GEO | 2023/10/23

REPOSITORIES: GEO

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Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [RNA-seq]

Project description:Investigate the role of topoisomerase 1 in the response to oxidative stress

2023-10-23 | GSE227183 | GEO

Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [Mnase-seq]

Project description:Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [Mnase-seq]

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Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery.

Project description:Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery.

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Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery.

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-10-23 | GSE227184 | GEO

Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [RNA-seq]

Project description:Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [RNA-seq]

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Topoisomerase I Poisoning by Electrophiles Derived from Oxidative Stress

Project description:The cancer target enyzme topoisomerase 1 transiently cleaves one strand of chromosomal DNA to relax accumulated strain that can prevent transcription, replication or chromatin assembly. The topoisomerase 1 poison camptothecin and its synthetic analogs are widely used chemotherapeutics that act by trapping the enzyme on DNA in a ‘covalent complex’, resulting in persistent DNA damage and cell death. The prevailing model, interfacial inhibition, contends that the covalent complex is trapped by drug binding alone. In contrast, here we show that camptothecins produce extensive oxidative stress and that topoisomerase 1 is reactive with electrophilic second messengers of oxidative damage. We show that blocking oxidative stress in cells inhibits covalent complex formation by camptothecin, while electrophiles such as 4-hydroxynonenal are able to induce covalent complex formation in cells on their own. Towards mechanism of action, we show that 4-hydroxynonenal electrophilically modifies a cysteine within the DNA-binding active site of human topoisomerase 1. Taken together, our results suggest a mechanism in which oxidative stress mediates the effects of many topoisomerase 1 poisons, and suggest that this critical DNA-regulating enzyme may have a dual role as a sensor of cellular redox stress, linking oxidative stress to DNA damage response in cancer cells.

2021-03-24 | PXD018549 | Pride

Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress [Mnase-Seq]

Project description:Transcription generates superhelical stress in DNA that poses problems for genome stability, but determining when and where such stress arises within chromosomes is challenging. Here, using G1-arrested S. cerevisiae cells, and employing rapid fixation and ultra-sensitive enrichment, we utilise the physiological activity of endogenous topoisomerase 2 (Top2) as a probe of transcription-induced superhelicity. We demonstrate that Top2 activity is surprisingly uncorrelated with transcriptional activity, suggesting that superhelical stress is obscured from Top2 within chromatin in vivo. We test this idea using osmotic perturbation—a treatment that transiently destabilises chromatin in vivo—revealing that Top2 activity redistributes within sub-minute timescales into broad zones patterned by long genes, convergent gene arrays, and transposon elements—and also by acute transcriptional induction. We propose that latent superhelical stress is normally absorbed by the intrinsic topological buffering capacity of chromatin, helping to avoid spurious topoisomerase activity arising within the essential coding regions of the genome.

2024-12-01 | GSE280155 | GEO

Quantitative MNase-seq accurately maps nucleosome occupancy levels.

Project description:Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, its aggressive endo-/exo-nuclease activities make MNase-seq unreliable for determining nucleosome occupancies, because cleavages within linker regions produce oligo- and mono-nucleosomes, whereas cleavages within nucleosomes destroy them. Here, we introduce a theoretical framework for predicting nucleosome occupancies and an experimental protocol with appropriate spike-in normalization that confirms our theory and provides accurate occupancy levels over an MNase digestion time course. As with human cells, we observe no overall differences in nucleosome occupancies between Drosophila euchromatin and heterochromatin, which implies that heterochromatic compaction does not reduce MNase accessibility of linker DNA.

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MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.

Project description:Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome placement, usually measured by quantifying protection of DNA from enzymatic digestion, can regulate accessibility. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC (MNase accessibility), quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both nucleosome location and accessibility in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares histone and non-histone protection. We find that changes in accessibility at enhancers, promoters and other regulatory regions do not correlate with changes in nucleosome occupancy. Moreover, high nucleosome occupancy does not necessarily preclude high accessibility, which reveals novel principles of chromatin regulation.

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Co-ordinate inhibiton of autism candidate genes by topoisomerase inhibitors [array]

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

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