The Enrichment and Regulation of High-methylated CpG sites in CGI Border in ARPE-19 [RNA-seq]
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ABSTRACT:
PROVIDER: PRJNA735529 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14744462_1.fastq.gz | Fastqsanger.gz | |||
| SRR14744462_2.fastq.gz | Fastqsanger.gz | |||
| SRR14892928_1.fastq.gz | Fastqsanger.gz | |||
| SRR14892928_2.fastq.gz | Fastqsanger.gz | |||
| SRR14892929_1.fastq.gz | Fastqsanger.gz |
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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.
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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.
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Project description:The Enrichment and Regulation of High-methylated CpG sites in CGI Border in ARPE-19 [MNase-seq]
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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 ARPE-19 cells were treated with 1μM adriamycin for 24 h compared with control
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Project description:Methylated DNA enrichment is a key step in a microarray based genome-wide methylation profiling study, and even for future high-throughput sequencing based methylome analysis. In order to evaluate the sensitivity and accuracy of methylated DNA enrichment, we investigated and optimized a number of important parameters to improve the performance of several enrichment assays, including differential methylation hybridization (DMH), microarray-based methylation assessment of single samples (MMASS), and methylated DNA immunoprecipitation (MeDIP). With advantages and disadvantages unique to each approach, we found that assays based on methylation-sensitive enzyme digestion and those based on immunoprecipitation detected different methylated DNA fragments, indicating that they are complementary in their relative ability to detect methylation differences. Our study provides the first comprehensive evaluation for widely used methodologies for methylated DNA enrichment, and could be helpful for developing a cost effective approach for DNA methylation profiling.
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Project description:X chromosome inactivation involves multiple levels of chromatin modification, established progressively and in a stepwise manner during early development. The chromosomal protein Smchd1 has recently been shown to play an important role in DNA methylation of CpG islands (CGIs), a late step in the X inactivation pathway required for long-term stability of gene silencing. Here we show that inactive X chromosome (Xi) CGI methylation can occur via either Smchd1 dependent or independent pathways. Smchd1 dependent CGI methylation, the primary pathway, is acquired gradually over an extended period, whereas Smchd1 independent CGI methylation occurs rapidly after the onset of X inactivation. The de novo methyltransferase Dnmt3b is required for methylation of both classes of CGI, whereas Dnmt3a and Dnmt3L are dispensable. Xi CGIs methylated by these distinct pathways differ in respect to their sequence characteristics and immediate chromosomal environment. We discuss the implications of these results for understanding CGI methylation during development. Examination of CpG methylated DNA from wild type and smchd1 null male and female somatic cells and female ES cells differentiated for either 7 or 10 days. Duplicate samples of each type were generated.
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Project description:Stable maintenance of cytosine methylation is essential for mammalian biological processes such as gene transcription. This study introduced a RRBS-based quantitative method to identify CpG sites of high methylation fidelity (especially those 100% methylation fidelity sites). To separate the 100% methylation fidelity sites , we cultured the ARPE-19, Jurkat and SW1353 cells for lasting 10 generations, and we detected the methylation level of each CpG sites in the 20th generation and the 30th generation by performing reduced representation bisulfite sequencing (RRBS), to obtain the 100% methylation fidelity sites. The result shows that the number of overlapped fidelity methylation CpG sites of the two different time is smaller than number of each generation. Our results also showed that the proportion of high-fidelity 100% methylated sites in Jurkat and ARPE-19 cells is about 4.4% and 8.9%, and the proportion in SW1353 cells is 1.98%. The fidelity methylation sites obtained by the comparison of the two different time periods are the truly unchanged CpG sites during cell passage, which improves the reliability of the fidelity methylation sites. In summary, we provide new insights into the DNA methylation fidelity study.
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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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