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Mus musculus

ABSTRACT: Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion (SCL-exo)

PROVIDER: PRJNA289245 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2090190.fastq.gz	Fastqsanger.gz
	SRR2090184.fastq.gz	Fastqsanger.gz
	SRR2090185.fastq.gz	Fastqsanger.gz
	SRR2090186.fastq.gz	Fastqsanger.gz
	SRR2090187.fastq.gz	Fastqsanger.gz

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Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion (SCL-exo)

Project description:We report the setup of a new method to map 5-hydroxymethylcytosine (5hmC) genome-wide at CpG resolution. The method combines selective chemical labeling by 5hmC b-glucosyltransferase and exonuclease digestion of the DNA molecules bound to streptavidin beads after biotinylation of the 5-glucosylmethylcytosines. Associated with a straightforward bioinformatic analysis, this new procedure provides a cost-effective and fast method for mapping 5hmC at high resolution.

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Project description:We report the genomic localization of 5-hydroxymethylcytosines in multiple myeloma patients through the use of selective chemical labeling (SCL) and exonuclease digestion. Data highlighted super-enhancers and enhancers specifically undergoing active DNA demethylation in multiple myeloma cells.

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A Sensitive Approach to Map Genome-wide 5-Hydroxymethylcytosine and 5-Formylcytosine at Single-base Resolution

Project description:Mapping genome-wide 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) at single-base resolution is important to understand their biological functions. We present a cost-efficient mapping method that combines 5hmC-specific restriction enzyme PvuRts1I with a 5hmC enrichment method. The sensitive method enables detection of low abundant 5hmC sites, providing a more complete 5hmC landscape than available bisulfite-based methods. This method generated the first genome-wide 5fC map at single-base resolution. Parallel analyses revealed that 5hmC and 5fC existed with lower abundance and more dynamically in non-CpG context than in CpG context. In the genic region, distribution of 5hmCpG and 5fCpG differed from 5hmCH and 5fCH (H=A, T, C). 5hmC and 5fC were distributed distinctly at regulatory protein-DNA binding sites, depleted in permissive transcription factor binding sites, and enriched at active and poised enhancers. This sensitive bisulfite-conversion free method can be applied to biological samples with limited starting material or low abundance of cytosine modifications. Sensitive mapping of genome-wide 5-hydroxymethylcytosine and 5-formylcytosine in mouse embryonic stem cell at single-base resolution by combining 5-hydroxymethylcytosine specific restriction enzyme PvuRts1I and 5-hydroxymethylcytosine enrichment method (selective chemical labeling or SEAL)

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Project description:Mapping of 5-hydroxymethylcytosine by selective chemical labeling (SCL-seq) in human naive B cells and in vitro differentiated plasmablasts (P1 cells) [HTS]

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