Evidence That Three Classes of Methylomes Specific for Stem, Somatic and Transformed Cells Are Set by Three Independent Mechanisms
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ABSTRACT:
PROVIDER: PRJNA335850 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3987330_1.fastq.gz | Fastqsanger.gz | |||
| SRR3987330_2.fastq.gz | Fastqsanger.gz | |||
| SRR3987420_1.fastq.gz | Fastqsanger.gz | |||
| SRR3987420_2.fastq.gz | Fastqsanger.gz | |||
| SRR3987331_1.fastq.gz | Fastqsanger.gz |
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Project description:Whole genome-bisulfite sequencing has revealed that methylomes differ dramatically in a cell type-specific manner. However, the global mechanisms of maintenance of DNA methylation patterns and their functional consequences are not clear. Using a combination of novel haplotype-resolved methylomes and publicly available data, we show that three distinct classes of methylomes that differ by the proportion of partially and highly methylated domains are characteristic of stem and progenitor, somatic and transformed cells. We provide evidence that three mechanisms can account for most of the differences between these three classes of methylomes. The first, protection of promoters and cis-acting regulatory elements from DNA methylation by DNA-binding proteins, keeps regulatory elements unmethylated. The second, DNA replication-associated maintenance of DNA methylation, is highly efficient in stem cells, moderately efficient in somatic cells, and very inefficient in transformed cells, and sets variable basal levels of methylation characteristic of the partially methylated domains of each cell type. The third, transcriptional elongation-associated gene-body DNA methylation is responsible for the formation of highly methylated domains in somatic and transformed cells. We show that partitioning of the genome into partially and highly methylated domains is associated with different mechanisms of gene silencing.
2019-07-23 | GSE84999 | GEO
Project description:Whole genome-bisulfite sequencing has revealed that methylomes differ dramatically in a cell type-specific manner. However, the global mechanisms of maintenance of DNA methylation patterns and their functional consequences are not clear. Using a combination of novel haplotype-resolved methylomes and publicly available data, we show that three distinct classes of methylomes that differ by the proportion of partially and highly methylated domains are characteristic of stem and progenitor, somatic and transformed cells. We provide evidence that three mechanisms can account for most of the differences between these three classes of methylomes. The first, protection of promoters and cis-acting regulatory elements from DNA methylation by DNA-binding proteins, keeps regulatory elements unmethylated. The second, DNA replication-associated maintenance of DNA methylation, is highly efficient in stem cells, moderately efficient in somatic cells, and very inefficient in transformed cells, and sets variable basal levels of methylation characteristic of the partially methylated domains of each cell type. The third, transcriptional elongation-associated gene-body DNA methylation is responsible for the formation of highly methylated domains in somatic and transformed cells. We show that partitioning of the genome into partially and highly methylated domains is associated with different mechanisms of gene silencing.
2019-07-23 | GSE84998 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-07-23 | GSE85000 | GEO
Project description:As the most studied type of epigenetic modifications found in many taxa, DNA methylation has been confirmed to play a crucial role in transposon silencing, transcriptional regulation and thus phenotypic variation, as well as rapid adaption to changing environments. To fully understand the methylome variation in Trichinella, here, we report 12 single-base resolution methylomes of three life stages using WGBS. By comparative epigenomics, we observe that the methylome variation in Trichinella is significantly divergent and host-related. By comparative epigenomics, we observe that the methylome variation in Trichinella is significantly divergent and host-related. By comparing DNA methylation patterns between different host classes of species, we found a fraction of parasitism-related genes under epigenetic regulation, such as G-protein-coupled receptor, DNaseII and ligand-gated chloride channel. Moreover, we also reveal associations between methylation divergence and genetic basis, including nucleotide variant and structural variation.
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare distinct immunostimulatory activities of three classes of CpG ODNs in B cells using RNA-seq. mRNA profiles of murine B cells induced by three classes of CpG ODNs were generated by RNA-Seq studies. Methods: mRNA profiles of murine B cells induced by three classes of CpG ODNs were generated by deep sequencing, in triplicate, using BGISEQ. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: HISAT based on Burrows-Wheeler transform and Ferragina-Manzini and Bowtie2 followed by RSEM. Results: Using an optimized data analysis workflow, we mapped > 60 million total clean reads per sample to the mouse genome (build mm10), with a clean reads Q20 score >97% and a mapping rate to the reference genome of each sample varying from 89.33% to 93.29%. The Pearson correlation coefficient between each sample revealed that the all samples had a high correlation. In particular, CpG-B and CpG-C have the highest correlation. A total of 28,020 genes were detected as being expressed. More than 10,000 genes were downregulated and 1,000 genes were upregulated in CpG ODNs stimulated groups relative to control group, with a fold change ≥ 2 and Q value <0.001. In addition, only 91 genes were upregulated and 99 genes were downregulated in CpG-C group relative to CpG-B group. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes uncovered several genes that may contribute to characterize the features of three classes of CpG ODNs in B cells. Conclusions: Our study represents the first detailed analysis of B-cell transcriptomes stimulated with three classes of CpG ODNs, with biological replicates, generated by RNA-seq technology.
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare distinct immunostimulatory activities of three classes of CpG ODNs in pDCs using RNA-seq. mRNA profiles of murine pDCs induced by three classes of CpG ODNs were generated by RNA-Seq studies. Methods: mRNA profiles of murine pDCs induced by three classes of CpG ODNs were generated by deep sequencing, in triplicate, using Illumina Hiseq Xten. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: HISAT based on Burrows-Wheeler transform and Ferragina-Manzini and Bowtie2 followed by RSEM. Results: Using an optimized data analysis workflow, we mapped > 60 million total clean reads per sample to the mouse genome (build mm10), with a clean reads Q20 score > 98.58% and a mapping rate to the reference genome of each sample varying from 92.3% to 96.56%. The Pearson correlation coefficient between each sample revealed that CpG-A and CpG-C have the highest correlation. A total of 21,573 genes were detected as being expressed. More than 5,000 genes were downregulated and 2,000 genes were upregulated in CpG ODNs stimulated groups relative to control group, with a fold change ≥ 2 and Q value <0.001. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes uncovered several genes that may contribute to characterize the features of three classes of CpG ODNs in pDCs. Conclusions: Our study represents the first detailed analysis of pDC transcriptomes stimulated with three classes of CpG ODNs, with biological replicates, generated by RNA-seq technology.
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Project description:12 single-base resolution methylomes of three life stages using WGBS
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Project description:Evidence That Three Classes of Methylomes Specific for Stem, Somatic and Transformed Cells Are Set by Three Independent Mechanisms (Methyl-Seq)
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Project description:Evidence That Three Classes of Methylomes Specific for Stem, Somatic and Transformed Cells Are Set by Three Independent Mechanisms (RNA-Seq)
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