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Selective identification of epigenetic regulators at methylated genomic sites by SelectID [ChIP-seq]

ABSTRACT: Selective identification of epigenetic regulators at methylated genomic sites by SelectID [ChIP-seq]

PROVIDER: PRJNA1152514 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30398900_1.fastq.gz	Fastqsanger.gz
	SRR30398900_2.fastq.gz	Fastqsanger.gz
	SRR30398901_1.fastq.gz	Fastqsanger.gz
	SRR30398901_2.fastq.gz	Fastqsanger.gz
	SRR30398902_1.fastq.gz	Fastqsanger.gz

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Selective identification of epigenetic regulators at methylated genomic sites by SelectID [RNA-seq]

Project description:Selective identification of epigenetic regulators at methylated genomic sites by SelectID [RNA-seq]

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Selective identification of epigenetic regulators at methylated genomic sites

Project description:We applied SelectID coupled with the ultra-sensitive micro-DIA approach to enrich the associated proteins of Chromosome 9 satellite region and methylated LINE-1 elements.

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Selective identification of epigenetic regulators at methylated genomic sites by SelectID [ChIP-seq]

Project description:DNA methylation is a significant component in proximal chromatin regulation and plays crucial roles in regulating gene expression and maintaining the repressive state of retrotransposon elements. However, accurate profiling of the proteomics which simultaneously identifies specific DNA sequences and their associated epigenetic modifications remains a challenge. Here, we report SelectID, which introduced methylated DNA binding domain into dCas9-mediated proximity labeling system to enable in situ protein capture at repetitive elements with 5-methylcytosine (5mC) modifications. SelectID were demonstrated as feasible as dCas9-TurboID system at specific DNA methylation regions, such as the chromosome 9 satellite. Using SelectID, we successfully identified CHD4 as potential repressors of methylated LINE-1 retrotransposon through direct binding at the 5’UTR of young LINE-1 elements. Overall, our SelectID approach has opened up new avenues for uncovering potential regulators of specific DNA regions with DNA methylation, which will greatly facilitate future studies on epigenetic regulation.

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Selective identification of epigenetic regulators at methylated genomic sites by SelectID [RNA-seq]

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Project description:Herein, we presented an antibody-free strategy termed Selective Release of Methylated Sites from Immobilized Tryptic Peptides (SRMs-ITP), which achieves high enrichment efficiency while enabling the simultaneous analysis of all five methylation states of KR.

2025-03-17 | PXD061946 |

Selective identification of epigenetic regulators at methylated genomic sites by SelectID

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Identification of differentially methylated sites in COPD by exposure to biomass smoke

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Identification of methylated sites in BT-549 cells affected by thymoquinone treatment

Project description:Identification of methylated sites in BT-549 cells affected by thymoquinone treatment

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Identification of methylated sites in BT-549 cells affected by thymoquinone treatment

Project description:BT-549 cells were treated with thymoquinone for 6 h and chromatin immune-precipitation (ChIP) was performed using anti- MBD1 antibody (Abcam, USA). Anti-MBD1 could precipitate specific genomic region, which are methylated. The ChIP products were sequenced by library construction and bioinformatics analysis. The gene ontology (GO) analysis for multiple pathways was performed. The genomic methylated regions affected by TQ treatment were identified.

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The Enrichment and Regulation of High-methylated CpG sites in CGI Border in ARPE-19 [RNA-seq]

Project description:Stable maintenance of cytosine methylation is essential for mammalian biological processes such as gene transcription. To investigate the relationship of stably high methylation sites with gene expression, we cultured the ARPE-19 for lasting 10 generations and performed reduced representation bisulfite sequencing (RRBS) to obtain the highly methylated sites. Then we analyzed the characters of highly methylated sites and detected the transcription level of the cells. After filtered the low methylated CpG island (CGI), we found that highly methylated CpG sites had a preference for CGI boundary. In the promoter CGI, only in the condition as the gene expression is inhibited and the promoter CGI is at a high methylation level, a significant enrichment of the highly methylated sites is observed in the promoter CGI boundary. Our results showed that the enrichment of high methylation sites at the boundary of the CGI in the promoter region would have a significant inhibitory effect on the gene expression. In summary, we provide new insights into the regulatory mechanisms of DNA methylation.

2021-06-07 | GSE176234 | GEO

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