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Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [RNA-seq]

ABSTRACT: Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [RNA-seq]

PROVIDER: PRJNA605248 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11040140.fastq.gz	Fastqsanger.gz
	SRR11040141.fastq.gz	Fastqsanger.gz
	SRR11040142.fastq.gz	Fastqsanger.gz
	SRR11040143.fastq.gz	Fastqsanger.gz
	SRR11040144.fastq.gz	Fastqsanger.gz

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Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing

Project description:Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing

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Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [MBD-seq]

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Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [ChIP-Seq]

Project description:Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [ChIP-Seq]

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Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [ChIP-Seq]

Project description:The aim of this study was to investigate the stability of DNA methylation, the dynamics of different histone modifications and the changes in expression after genome-wide introduction of DNA methylation in promotor CpG islands. Therefore, the catalytic domain of DNMT3A was fused to a zinc finger protein and expressed for three days to globally introduce de novo DNA methylation and subsequently, the changes in the epigenome were monitored for up to eleven days.

2020-11-10 | GSE144928 | GEO

Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [RNA-seq]

2020-11-10 | GSE144903 | GEO

Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [MBD-seq]

2020-11-10 | GSE144331 | GEO

A modular dCas9-based recruitment platform for combinatorial epigenome editing

Project description:Targeted epigenome editing tools allow precise manipulation and investigation of genome modifications, however they often display high context dependency and variable efficacy between target genes and cell types. While systems that simultaneously recruit multiple distinct ‘effector’ chromatin regulators can improve efficacy, they generally lack control over effector composition and spatial organisation. To overcome this we have created a modular combinatorial epigenome editing platform, called SSSavi. This system is an interchangeable and reconfigurable docking platform fused to dCas9 that enables simultaneous recruitment of up to four different effectors, allowing precise control of effector composition and spatial ordering. We demonstrate the activity and specificity of the SSSavi system and compare it to existing multi-effector targeting systems, demonstrating its efficacy. Furthermore, we demonstrate the importance of the effector recruitment spatial ordering for effective transcriptional regulation. Together, the SSSavi system enables exploration of combinatorial effector co-recruitment to enhance manipulation of chromatin contexts previously resistant to targeted editing.

2023-11-02 | GSE241460 | GEO

Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing.

Project description:Chromatin properties are regulated by complex networks of epigenome modifications. Currently, it is unclear how these modifications interact and if they control downstream effects such as gene expression. We employed promiscuous chromatin binding of a zinc finger fused catalytic domain of DNMT3A to introduce DNA methylation in HEK293 cells at many CpG islands (CGIs) and systematically investigated the dynamics of the introduced DNA methylation and the consequent changes of the epigenome network. We observed efficient methylation at thousands of CGIs, but it was unstable at about 90% of them, highlighting the power of genome-wide molecular processes that protect CGIs against DNA methylation. Partially stable methylation was observed at about 1000 CGIs, which showed enrichment in H3K27me3. Globally, the introduced DNA methylation strongly correlated with a decrease in gene expression indicating a direct effect. Similarly, global but transient reductions in H3K4me3 and H3K27ac were observed after DNA methylation but no changes were found for H3K9me3 and H3K36me3. Our data provide a global and time-resolved view on the network of epigenome modifications, their connections with DNA methylation and the responses triggered by artificial DNA methylation revealing a direct repressive effect of DNA methylation in CGIs on H3K4me3, histone acetylation, and gene expression.

| S-EPMC7797067 | biostudies-literature

Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing

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

2020-11-10 | GSE144904 | GEO

Investigation of RNA editing sites within bound regions of RNA-binding proteins

Project description:Studies in epitranscriptomics indicates that RNA is modified by a variety of enzymes. Among these RNA modifications, A-to-I RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA-seq data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNAEditor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affects the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncover that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands are examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, HuR, was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme ADAR compared to the control—suggesting that the presence of RNA editing islands influences HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP-RNA interactions—a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.

2019-11-30 | GSE141095 | GEO

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