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Genomic RNA-DNA duplexes in mitotically arrested cells

ABSTRACT: Genomic RNA-DNA duplexes in mitotically arrested cells

PROVIDER: PRJNA685178 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13253352_1.fastq.gz	Fastqsanger.gz
	SRR13253352_2.fastq.gz	Fastqsanger.gz
	SRR13253353_1.fastq.gz	Fastqsanger.gz
	SRR13253353_2.fastq.gz	Fastqsanger.gz
	SRR13253354_1.fastq.gz	Fastqsanger.gz

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Genomic RNA-DNA duplexes in mitotically arrested cells

Project description:RNA-DNA duplexes have been extensively catalogued in interphase cells, but relatively little is known about the genomic loci of these duplexes in mitotic cells. We compared RNA-DNA duplexes in DLD1 cells arrested in mitosis to libraries previously published in asynchronous HEK293T cells prepared with the same protocols, and processed with the same bioinformatic pipeline. We also observed that Aurora B inhibitors increased the immunofluorescence signal for RNA-DNA duplexes in mitotic cells, so we tested the effect of Aurora B inhibition on genomic enrichment of RNA-DNA duplexes.

2021-02-28 | GSE163197 | GEO

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Project description:genomic localization of the budding yeast cohesin complex was mapped in mitotically arrested cells by Mcd1 ChIP followed by hybridization to high-density tiled microarrays Cells were synchronized first in G1 and then released into media containing the microtubule poison nocodazole. Cells were fixed and processed for ChIP once arrested as large-budded cells. Immunoprecipitated DNA and total genomic DNA not subjected to immunoprecipitation were competitively hybridized to Nimblegen whole genome arrays.

2009-09-30 | E-GEOD-18021 | biostudies-arrayexpress

Budding yeast cohesin (Mcd1) distribution in mitotically arrested cells

Project description:genomic localization of the budding yeast cohesin complex was mapped in mitotically arrested cells by Mcd1 ChIP followed by hybridization to high-density tiled microarrays

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Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells

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Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells

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Investigating global transcript dynamics in mitotically arrested budding yeast cells

Project description:Transcript dynamics in mitotic exit mutants in the S. cerevisiae BF264-15D strain background. We examined the extent to which periodic cell-cycle transcription persisted in cells arrested in anaphase with intermediate level of B-cyclins.

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Brn2 (POU3F2) ChIP-seq data obtained from asynchronous or mitotically arrested mouse neural stem/progenitor cells

Project description:Brn2 (POU3F2) ChIP-seq data obtained from asynchronous or mitotically arrested mouse neural stem/progenitor cells

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Brn2 (POU3F2) ChIP-seq data obtained from asynchronous or mitotically arrested mouse neural stem/progenitor cells

Project description:dataset contains 8 samples: 2 asynchronous and 2 mitotically synchronized populations (one with 90% and another with 95% mitotic purity) and 4 corresponding inputs. Cells were synchonized for 10h with colchicine at 330nM. asyncronous samples (interphase) were sonicated and prepared in parallel with same cell number as the corresponding mitotic samples. Fetal neural stem/progenitor cells were obtained from mouse telencephalon (ventral region) at E13.5. This data generated 4 genome-wide binding profiles corresponding to Brn2 (POU3f2) binding sites, aligned to MM9 mus musculus dataset.

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Project description:In mammals, the dynamics of DNA methylation, in particular the regulated, active removal of cytosine methylation has remained a mystery, partly due to the lack of appropriate model systems to study DNA demethylation. Previous work largely focused on proliferating cell types that had been mitotically arrested using pharmacological inhibitors to distinguish between active and passive mechanisms of DNA demethylation. Here, we characterised this epigenetic phenomenon in a natural setting of post-mitotic cells: the differentiation of human peripheral blood monocytes into macrophages or dendritic cells which proceeds without cell division. We identified many novel examples of active DNA demethylation using a global, comparative CpG methylation profiling approach and characterised accompanying transcriptional and epigenetic events at these sites during monocytic differentiation. Keywords: MCIp-on-Chip; comparative genomic hybridization

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Loss of PFKFB4 induces cell death in mitotically arrested ovarian cancer cells.

Project description:Taxanes represent some of the most commonly used chemotherapeutic agents for ovarian cancer treatment. However, they are only effective in approximately 40% of patients. Novel therapeutic strategies are required to potentiate their effect and improve patient outcome. A hallmark of many cancers is the constitutive activation of the PI3K/AKT pathway, which drives cell survival and metabolism. We discovered a striking decrease in AKT activity coupled with a significant reduction in glucose 6-phosphate and ATP levels during mitotic arrest in the majority of ovarian cancer cell lines tested, indicating a potential metabolic vulnerability. A high-content siRNA screen to detect novel metabolic targets in mitotically arrested ovarian cancer cells identified the glycolytic enzyme PFKFB4. PFKFB4 depletion increased caspase 3/7 activity, and levels of reactive oxygen species only in mitotically arrested cells, and significantly enhanced mitotic cell death after paclitaxel treatment. Depletion of PFKFB3 demonstrated a similar phenotype. The observation that some ovarian cancer cells lose AKT activity during mitotic arrest and become vulnerable to metabolic targeting is a new concept in cancer therapy. Thus, combining mitotic-targeted therapies with glycolytic inhibitors may act to potentiate the effects of antimitotics in ovarian cancer through mitosis-specific cell death.

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