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

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

PROVIDER: PRJNA605353 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11040427.fastq.gz	Fastqsanger.gz
	SRR11040428.fastq.gz	Fastqsanger.gz
	SRR11040429_1.fastq.gz	Fastqsanger.gz
	SRR11040429_2.fastq.gz	Fastqsanger.gz
	SRR11040430_1.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 [RNA-seq]

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

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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.

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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.

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Project description:Epigenetic aberration is one of the major driving factors in human cancer, often leading to acquired resistance to chemotherapies. Various chemical epigenetic modulators have been reported. Nonetheless, outcomes from animal models and clinical trials have underscored the substantial setbacks attributed to pronounced on- and off-target toxicities. To address these challenges, CRISPR/dCas9 technology emerges as a potent tool for precise epigenetic regulation. This relies on the co-expression of exogenous epigenetic modulator proteins, presenting technical challenges during preparation and delivery, as well as potential undesirable side effects. Recently, our research demonstrated that Cas9 tagged with the FCPF-peptide motif could be recognized by perfluoro biphenyl (PFB) derivatives. Here, we integrated the FCPF-tag into dCas9 and established a chemically inducible platform for epigenome editing, called Chem-CRISPR/dCas9FCPF. We designed a series of chemical inhibitor-PFB conjugates targeting various epigenetic modulator proteins. Focusing on JQ1, a BRD4 inhibitor, we demonstrate that c-MYC-sgRNA-guided JQ1-PFB specifically inhibits BRD4 in close proximity to the c-MYC promoter/enhancer, thereby effectively repressing the intricate transcription networks orchestrated by c-MYC. In conclusion, our Chem-CRISPR/dCas9FCPF platform presents a promising alternative to conventional fusion protein systems. It replaces exogenous epigenetic modulator proteins with chemical inhibitors, offering a highly efficient and precise approach to epigenome editing.

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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.

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