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Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [RNA-seq]

ABSTRACT: Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [RNA-seq]

PROVIDER: PRJNA896533 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22128729_1.fastq.gz	Fastqsanger.gz
	SRR22128729_2.fastq.gz	Fastqsanger.gz
	SRR22128730_1.fastq.gz	Fastqsanger.gz
	SRR22128730_2.fastq.gz	Fastqsanger.gz
	SRR22128731_1.fastq.gz	Fastqsanger.gz

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Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions

Project description:Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions

| PRJNA896526 | ENA

Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [EPIC]

Project description:Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [EPIC]

| PRJNA896534 | ENA

Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [Promoter Capture Hi-C]

Project description:Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [Promoter Capture Hi-C]

| PRJNA896535 | ENA

Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [EPIC]

Project description:DNA methylation is one of the most important epigenetic marks and changes in DNA methylation patterns have been associated with many different types of cancer. Recently, three-dimensional (3D) genome organisation has been demonstrated to play a fundamental role in gene regulation. Determining the interplay between DNA methylation and 3D chromatin structure and function is challenging due to the extreme complexity of epigenetic regulation. To study the impact of DNA methylation on 3D genome organization, we performed a time-course of Decitabine treatment in tamoxifen-resistant MCF7 (TAMR) cells. Decitabine was applied daily for 7 days, followed by “recovery” up to 28 days and DNA methylation (EPIC), gene expression (RNA-seq) and promoter-enhancer interactions (PCHi-C) were assessed on day 7 post-Decitabine- and Vehicle-treatment and day 28 “Recovery” and Vehicle treatment in duplicate. Our data revealed a functional link between DNA hypomethylation at distal enhancer regions, enhancer-promoter interactions, and gene regulation.

2023-08-07 | GSE216986 | GEO

Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [Promoter Capture Hi-C]

2023-08-08 | GSE216987 | GEO

Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [RNA-seq]

2023-08-08 | GSE216988 | GEO

The Mediator complex regulates enhancer-promoter interactions

Project description:The Mediator complex regulates enhancer-promoter interactions

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Enhancer-promoter interactions in acheiropodia patient's cells

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Enhancer Cis Elements Instruct Promoter-Enhancer Interaction, Promoter-Enhancer Insulation and Compartmental Segregation

Project description:Enhancer Cis Elements Instruct Promoter-Enhancer Interaction, Promoter-Enhancer Insulation and Compartmental Segregation

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Increased Enhancer—Promoter Interactions during Developmental Enhancer Activation in Mammals

Project description:Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here, we investigate the 3D conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. 61% of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer–promoter and enhancer–enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer–promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general significance of enhancer–promoter physical proximity for developmental gene activation in mammals.

2024-01-03 | GSE217078 | GEO

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