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Homo sapiens

ABSTRACT: DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [BS-Seq]

PROVIDER: PRJNA382984 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5448840.fastq.gz	Fastqsanger.gz
	SRR5448831_1.fastq.gz	Fastqsanger.gz
	SRR5448831_2.fastq.gz	Fastqsanger.gz
	SRR5448841.fastq.gz	Fastqsanger.gz
	SRR5448832_1.fastq.gz	Fastqsanger.gz

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DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [RNA-Seq]

Project description:We demonstrate that dCas9-SunTag-DNMT3A dramatically increased CpG methylation at the HOXA5 locus in human embryonic kidney 293T cells (HEK293T). Furthermore, using a single sgRNA, dCas9-SunTag-DNMT3A was able to methylate a 4.5 kb genomic region and repress HOXA5 gene expression. Reduced representation bisulfite sequencing (RRBS) and RNA-seq showed that dCas9-SunTag-DNMT3A methylated regions of interest with minimal impact on the global DNA methylome and transcriptome.

2017-08-22 | GSE97815 | GEO

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DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [BS-Seq]

Project description:Here, we demonstrate that dCas9-SunTag-DNMT3A dramatically increased CpG methylation at the HOXA5 locus in human embryonic kidney 293T cells (HEK293T). Furthermore, using a single sgRNA, dCas9-SunTag-DNMT3A was able to methylate a 4.5 kb genomic region and repress HOXA5 gene expression. Reduced representation bisulfite sequencing (RRBS) and RNA-seq showed that dCas9-SunTag-DNMT3A methylated regions of interest with minimal impact on the global DNA methylome and transcriptome.

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Engineering of effector domains for targeted DNA methylation with reduced off-target effects

Project description:Epigenome editing is a promising technology, potentially allowing the stable reprogramming of gene expression profiles without alteration of the DNA sequence. Targeted DNA methylation has been successfully documented by many groups for silencing of selected genes, but recent publications have raised concerns regarding its specificity. In the current work, we developed new EpiEditors for programmable DNA methylation in cells with a high efficiency and improved specificity. First, we demonstrated that the dCas9-SunTag scaffold, which has been used earlier for signal amplification, can be combined with the DNMT3A-DNMT3L effector domain allowing a strong methylation at the target genomic locus. We demonstrated that off-target activity of this system is mainly due to untargeted freely diffusing DNMT3A-DNMT3L subunits. Therefore, we generated several DNMT3A variants containing mutations, which reduced their endogenous DNA binding strength. We analyzed the genome-wide DNA methylation of selected variants and confirmed a striking reduction of untargeted methylation. For all potential applications of targeted DNA methylation, the efficiency and specificity of the treatment are the key factors. By developing highly active targeted methylation systems with strongly improved specificity, our work contributes to the future applications of this approach.

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ChIP-seq of GFP-tagged dCoREST, dLSD1, dL(3)mbt and dG9a in D. melanogaster S2 cell lines

Project description:We employed CRISPR/Cas-mediated genome editing to generate S2 cell lines expressing GFP-tagged dCoREST, dL(3)mbt, dLSD1 and dG9a, respectively. This allowed us to determine the genome-wide binding profiles for these proteins by ChIP-seq using the same antibody (anti-GFP) in each case.

2019-11-04 | E-MTAB-8341 | biostudies-arrayexpress

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