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Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE215325 | GEO | 2023/03/31

REPOSITORIES: GEO

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Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters

Project description:To investigate the function of the doxorubicin treatment in differentiation expression of human genes, we performed gene expression profiling analysis using data obtained from RNA-seq of three different conditions: control (DMSO-treatment) and doxorubicin treatment (200 nM and 340 nM).

2023-03-31 | GSE215321 | GEO

Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters

Project description:To investigate the function of the TOP2 inhibitors treatment in binding of chromatin architecture factors, we performed ChIP-seq. We used chromatin from RPE1 cells treated with four different conditions: control (DMSO-treatment), doxorubicin treatment (200 nM and 340 nM) and ICRF193 treatment (5uM).

2023-03-31 | GSE215318 | GEO

Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters

Project description:To investigate the function of TOP2 on chromatin structure of human cells, we performed Hi-C using chromatin obtained from RPE1 cells.

2023-03-31 | GSE214912 | GEO

Doxorubicin enhances nucleosome turnover around promoters.

Project description:Doxorubicin is an anthracycline DNA intercalator that is among the most commonly used anticancer drugs. Doxorubicin causes DNA double-strand breaks in rapidly dividing cells, although whether it also affects general chromatin properties is unknown. Here, we use a metabolic labeling strategy to directly measure nucleosome turnover to examine the effect of doxorubicin on chromatin dynamics in squamous cell carcinoma cell lines derived from genetically defined mice. We find that doxorubicin enhances nucleosome turnover around gene promoters and that turnover correlates with gene expression level. Consistent with a direct action of doxorubicin, enhancement of nucleosome turnover around promoters gradually increases with time of exposure to the drug. Interestingly, enhancement occurs both in wild-type cells and in cells lacking either the p53 tumor suppressor gene or the master regulator of the DNA damage response, ATM, suggesting that doxorubicin action on nucleosome dynamics is independent of the DNA damage checkpoint. In addition, another anthracycline drug, aclarubicin, shows similar effects on enhancing nucleosome turnover around promoters. Our results suggest that anthracycline intercalation promotes nucleosome turnover around promoters by its effect on DNA topology, with possible implications for mechanisms of cell killing during cancer chemotherapy.

| S-EPMC3678987 | biostudies-literature

Doxorubicin enhances nucleosome turnover around promoters

Project description:We use a metabolic labeling strategy for directly measuring nucleosome turnover to examine the effect of doxorubicin on chromatin dynamics in squamous cell carcinoma cell lines derived from genetically defined mice. We find that doxorubicin enhances nucleosome turnover around gene promoters, and turnover correlates with gene expression level. Keywords: Chromatin affinity-purification on microarray 26 CATCH-IT arrays and 8 expression arrays.

2013-04-19 | E-GEOD-43753 | biostudies-arrayexpress

Doxorubicin enhances nucleosome turnover around promoters

2013-04-19 | GSE43753 | GEO

Cycles in spatial and temporal chromosomal organization driven by the circadian clock

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-08 | E-GEOD-49639 | biostudies-arrayexpress

Spatial genome re-organization between fetal and adult hematopoietic stem cells

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

2019-12-16 | GSE119201 | GEO

Antagonism between H3K27me3 and genome-lamina association drives atypical spatial genome organization in the totipotent embryo

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

2024-08-09 | GSE218598 | GEO

Genome Organization in and around the Nucleolus.

Project description:The nucleolus is the largest substructure in the nucleus, where ribosome biogenesis takes place, and forms around the nucleolar organizer regions (NORs) that comprise ribosomal RNA (rRNA) genes. Each cell contains hundreds of rRNA genes, which are organized in three distinct chromatin and transcriptional states-silent, inactive and active. Increasing evidence indicates that the role of the nucleolus and rRNA genes goes beyond the control of ribosome biogenesis. Recent results highlighted the nucleolus as a compartment for the location and regulation of repressive genomic domains and, together with the nuclear lamina, represents the hub for the organization of the inactive heterochromatin. In this review, we aim to describe the crosstalk between the nucleolus and the rest of the genome and how distinct rRNA gene chromatin states affect nucleolus structure and are implicated in genome stability, genome architecture, and cell fate decision.

| S-EPMC6628108 | biostudies-literature

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