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

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

PROVIDER: PRJNA735783 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14752109_1.fastq.gz	Fastqsanger.gz
	SRR14752109_2.fastq.gz	Fastqsanger.gz
	SRR14752110_1.fastq.gz	Fastqsanger.gz
	SRR14752110_2.fastq.gz	Fastqsanger.gz

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The Enrichment and Regulation of High-methylated CpG sites in CGI Border in ARPE-19 [MNase-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.

2021-06-08 | GSE176336 | GEO

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

2021-06-07 | GSE176234 | GEO

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

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

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ARPE-19_adriamycin_gene_expression

Project description:This study compared the gene expression change of ARPE-19 cells before and after adriamycin treatment ARPE-19 cells were treated with 1Î¼M adriamycin for 24 h compared with control

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ARPE-19_adriamycin_gene_expression

Project description:This study compared the gene expression change of ARPE-19 cells before and after adriamycin treatment

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BANP is an essential transcription factor that opens chromatin and activates CpG island regulated genes

Project description:While the majority of RNA polymerase II initiation events in mammalian genomes take place within CpG island (CGI) promoters, our understanding of their regulation remains limited. Here we combine single-molecule footprinting with interaction proteomics to identify BANP as a critical CGI regulator and the long sought-after TF that binds the orphan CGCG element in mouse and human. We show that BANP drives the activity of essential metabolic genes in the mouse genome in pluripotent and terminally differentiated cells. However, BANP binding is strongly repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for its absence at aberrantly methylated CGIs in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. Our results establish Banp as a critical activator and put forth a model whereby CGI promoter activity relies on methylation-sensitive TFs capable of chromatin opening.

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Project description:This study compared the gene expression change of ARPE-19 cells before and after adriamycin treatment

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Gene expression signitures in ARPE-19 cells treated with or without TGF-β1

Project description:To identify the dysregulated lncRNA and mRNA expression in ARPE-19 cells underwent EMT, we established a TGF-β1 induced EMT model of ARPE-19 cells. ARPE-19 cells were treated with or without 10 ng/ml TGF-β1 for 48 h. Total RNA are extracted and subjected to microarray assay (Arraystar Human LncRNA Microarray V3.0)

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Expression Data from DMSO or SRPIN803 treated ARPE-19 cells

Project description:We used microarrays to evaluate the effect of SRPIN803 on gene expression in ARPE-19 cells. ARPE-19 cells were treated with SRPIN803 (10 uM) or the negative control (0.1% DMSO) for 4 hours for Total RNA isolation and hybridization on Microarray.

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Project description:To characterize the potential molecular pathway(s) affected by iron treatment and identify the one(s) responsible for C3 induction, we performed a whole genome microarray on untreated ARPE-19 cells and cells treated with 250 ?M FAC for 48h/2d. Gene expression was compared between untreated and FAC-treated ARPE-19 cells, with three biological replicates in each.

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