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Reorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells

ABSTRACT: Reorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells

PROVIDER: PRJNA847983 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19627180_1.fastq.gz	Fastqsanger.gz
	SRR19627180_2.fastq.gz	Fastqsanger.gz
	SRR19627181_1.fastq.gz	Fastqsanger.gz
	SRR19627181_2.fastq.gz	Fastqsanger.gz
	SRR19627182_1.fastq.gz	Fastqsanger.gz

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Reorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells

Project description:Doxorubicin resistance remains a major therapeutic challenge leading to treatment failure and poor survival prognosis in breast cancer. Although doxorubicin induces massive changes in the transcriptional landscape accompanied by alterations of chromatin accessibility are well known, potential diagnostic or therapeutic targets associated with three-dimensional (3D) genome reorganization in doxorubicin-resistant breast cancer cells have not yet been systematically investigated. Here we performed integrated analyses combining in situ high-throughput chromosome conformation capture (Hi-C), ATAC-seq and mHi-C data on doxorubicin-resistant MCF7 human breast cancer cells compared to parental cells. It revealed that A/B compartment switching was positively correlated to genome-wide differential gene expression, and the genome was spatially reorganized into smaller topologically associating domains (TADs) and loops. We also revealed the contribution of increased chromatin accessibility and potential transcription factor families, including CTCF and BORIS, to gained TAD boundaries and loop anchors. Intriguingly, we observed two condensed genomic regions (~20kb) with decreased chromatin accessibility flanking TAD boundaries, which might play a critical role in the formation or maintenance of TADs. Moreover, we identified a number of gained and lost enhancer-promoter interactions associated with differentially expressed genes, including FA2H, FOXA1, JRKL and EZH, some of which involved in chromatin organization and breast cancer signaling pathways. This study uncovered a close connection between 3D genome reorganization, chromatin accessibility as well as gene transcription, and provides resources and novel insights into the epigenomic mechanisms with potential therapeutic implications for doxorubicin resistance in breast cancer.

2022-06-14 | GSE205874 | GEO

Reorganization of 3D chromatin architecture of rice genomes during heat stress (HiC)

Project description:Reorganization of 3D chromatin architecture of rice genomes during heat stress (HiC)

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Reorganization of 3D chromatin architecture of rice genomes during heat stress (Bisulfite-seq)

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Reorganization of 3D chromatin architecture of rice genomes during heat stress (ATAC-Seq)

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Reorganization of 3D chromatin architecture of rice genomes during heat stress (RNA-Seq)

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Reorganization of 3D chromatin architecture of rice genomes during heat stress (MeDIP-Seq)

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UV-induced reorganization of 3D genome mediates DNA damage response [RNA-Seq]

Project description:While it is well-established that UV radiation threatens genomic integrity, the precise mechanisms by which cells orchestrate DNA damage response and repair within the context of 3D genome architecture remain unclear. Here, we address this gap by investigating the UV-induced reorganization of the 3D genome and its critical role in mediating damage response. Employing temporal maps of contact matrices and transcriptional profiles, we illustrate the immediate and holistic changes in genome architecture post-irradiation, emphasizing the significance of this reconfiguration for effective DNA repair processes. We demonstrate that UV radiation triggers a comprehensive restructuring of the 3D genome structure at all levels, including loops, topologically associating domains and compartments. Through the analysis of DNA damage and excision repair maps, we uncover a correlation between genome folding, gene regulation, damage formation probability, and repair efficacy. We show that adaptive reorganization of the 3D genome is a key mediator of the damage response, providing new insights into the complex interplay of genomic structure and cellular defense mechanisms against UV-induced damage, thereby advancing our understanding of cellular resilience.

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UV-induced reorganization of 3D genome mediates DNA damage response [Hi-C]

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Project description:To establish a data-driven learning model of the temporal dynamics and 3D chromatin reorganization, we conducted tethered chromatin conformation (TCC) sequencing to examine 3D structure dynamics in estradiol (E2)-induced breast cancer MCF7 cells and Tamoxifen resistant breast cancer MCF7 cells.

2019-04-09 | GSE108787 | GEO

Temporal dynamic reorganization of 3D chromatin in hormone-induced breast cancer and endocrine resistance [T47D]

Project description:To establish a data-driven learning model of the temporal dynamics and 3D chromatin reorganization, we conducted tethered chromatin conformation (TCC) sequencing to examine 3D structure dynamics in estradiol (E2)-induced breast cancer T47D cells and Tamoxifen resistant breast cancer T47D cells.

2019-04-09 | GSE119890 | GEO

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