A human DNA methylation atlas reveals principles of cell type-specific methylation and identifies thousands of cell type-specific regulatory elements
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PROVIDER: PRJNA773951 | ENA |
REPOSITORIES: ENA
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Project description:DNA methylation is a fundamental epigenetic mark that governs chromatin organization, cell identity, and gene expression. Here we describe a human methylome atlas, based on deep whole-genome bisulfite sequencing of 39 cell types sorted from 205 healthy tissue samples. Replicates of the same cell type are >99.5% identical, demonstrating robustness of cell identity programs to genetic variation and environmental perturbation. Unsupervised clustering of the atlas recapitulates key elements of tissue ontogeny, and identifies methylation patterns retained since gastrulation. Loci uniquely unmethylated in an individual cell type often reside in transcriptional enhancers and contain DNA binding sites for tissue-specific transcriptional regulators. Uniquely methylated loci are rare and are enriched for CpG islands, polycomb targets, and CTCF binding sites, suggesting a role in shaping cell type-specific chromatin looping. The atlas provides an essential resource for interpretation of disease-associated genetic variants, and a wealth of potential tissue-specific biomarkers for use in liquid biopsies.
2022-03-02 | GSE186458 | GEO
Project description:DNA methylation, in concert with other epigenetic regulators, controls the accessibility of transcription factors to DNA. While comprehensively described in the development of neuronal progenitors, the role of DNA methylation/demethylation in neuronal lineage/subtype specification is not known. By profiling two distinct neuronal lineages, and five neuron subtypes in the hippocampus and striatum, we uncovered a set of five principles that govern DNA methylation dynamics in neurodevelopment. By dividing neurodevelopment to three alternating methylation and demethylation periods and applying the principles to each of these stages, we created a matrix that comprehensively describes the targets, genomic contexts, functional consequences and putative mechanisms of methylation/demethylation events. The overarching theme is that the developmental methylation program is remarkably similar in the hippocampal and striatal lineages, with significant divergence only occurring during subtype specification. Our matrix can be cross-referenced with disease-associated epigenetic changes to specify the possible events and underlying principles compromised in disease. Compared tissue from C57BL6 male animals at differenent developmental timepoints and regions for differences in DNA methylation and RNA expression. Additionally Dnmt3a conditional knockdown mice were used to determine role of Dnmt3a during development.
2016-02-20 | E-GEOD-72700 | biostudies-arrayexpress
Project description:DNA methylation, in concert with other epigenetic regulators, controls the accessibility of transcription factors to DNA. While comprehensively described in the development of neuronal progenitors, the role of DNA methylation/demethylation in neuronal lineage/subtype specification is not known. By profiling two distinct neuronal lineages, and five neuron subtypes in the hippocampus and striatum, we uncovered a set of five principles that govern DNA methylation dynamics in neurodevelopment. By dividing neurodevelopment to three alternating methylation and demethylation periods and applying the principles to each of these stages, we created a matrix that comprehensively describes the targets, genomic contexts, functional consequences and putative mechanisms of methylation/demethylation events. The overarching theme is that the developmental methylation program is remarkably similar in the hippocampal and striatal lineages, with significant divergence only occurring during subtype specification. Our matrix can be cross-referenced with disease-associated epigenetic changes to specify the possible events and underlying principles compromised in disease.
2016-02-20 | GSE72700 | GEO
Project description:RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
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Project description:Colorectal cancer is a common malignant tumor of the digestive tract. It is still a challenging task to detect colorectal cancer at an early stage. Studies have found that DNA methylation has a relationship with the occurrence and development of tumors. Singlera Genomics Inc. has invented the proprietary methyl-Titan sequencing technology and developed a detection method for colorectal cancer and advanced adenoma (Adenoma/Colorectal cancer Early detection, ACE) using the cancer-specific methylation markers. ACE is a blood-based non-invasive diagnostic technique. It has high compliance rate compared with colonoscopy, and sampling is more convenient than stool testing. It also has much higher sensitivity compared to existing blood testing methods.
The current study plans to use ACE method to analyze ctDNA in the blood for the cancer-specific DNA methylation markers to aid in the differential diagnosis of patients with colorectal cancer or adenoma. This technique will greatly reduce the discomfort in the diagnosis of suspected patients and improve the diagnosis of high-risk population of colorectal cancer.
The goals of this study are: 1) to establish a detection system based on plasma ctDNA methylation sequencing technology for the auxiliary diagnosis of colorectal cancer and adenoma, 2) to assess the diagnostic value of plasma ctDNA methylation signature for colorectal cancer and adenoma, and 3) to assess the association of plasma ctDNA methylation signals with colonoscopy results and pathological results of surgical specimens.
A total of 1300 patients (700 cases positive and 600 cases negative) aging between 45 and 80 years old will be enrolled. Colonoscopy will be performed to determine whether patients are positive or negative. Positive patients who need surgical resection will be further classified according to their surgical histopathological results. For negative patients, the type of lesion will be clarified. The plasma samples of all subjects will be analyzed for cancer-specific ctDNA methylation profiles. Based on the results of plasma ctDNA methylation test, the risks of colorectal cancer of the enrolled subjects are scored. Combined with the grouping information, the clinical application value of the cancer-specific methylation profile for early cancer diagnosis will be assessed.
| 2296221 | ecrin-mdr-crc
Project description:RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (CAGE)
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Project description:Cell-type-specific differential methylation in rheumatoid arthritis peripheral blood samples
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Project description:RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (RADICL-seq)
| PRJNA546285 | ENA
Project description:Methylation is a repressive modification of DNA prevalent throughout mammalian genomes yet mostly absent at CG rich stretches referred to as CGI. Here we identify their building principles by parallel genomic targeting of sequence libraries. Iterative insertions generated over 3,000 variants of genome-derived and artificial sequences at the same genomic site. Single molecule profiling of the methylation status of this collection allowed modeling the contribution of CG content and DNA binding factors towards the unmethylated state. It made the surprising prediction that the majority of CGs within endogenous islands are susceptible to methylation changes modulated by the presence of transcription factors, which is indeed confirmed by genome-wide methylation dynamics during multiple cellular differentiations. Our model further predicts blocks of constitutively unmethylated CGs independent from TF binding, which have a median size of ~300bp but are only present in half of all islands. Their constitutively unmethylated state is a hallmark of untransformed cells but their increased methylation is a specific and predictive feature of cancer. This study quantifies the two principal mechanisms governing methylation patterns in mammalian genomes. It provides a framework to interpret methylation data across normal and cancer samples and refines the concept of CpG islands. Methylation is a repressive modification of DNA prevalent throughout mammalian genomes yet mostly absent at CG rich stretches referred to as CGI. Here we identify their building principles by parallel genomic targeting of sequence libraries. Iterative insertions generated over 3,000 variants of genome-derived and artificial sequences at the same genomic site. Single molecule profiling of the methylation status of this collection allowed modeling the contribution of CG content and DNA binding factors towards the unmethylated state. It made the surprising prediction that the majority of CGs within endogenous islands are susceptible to methylation changes modulated by the presence of transcription factors, which is indeed confirmed by genome-wide methylation dynamics during multiple cellular differentiations. Our model further predicts blocks of constitutively unmethylated CGs independent from TF binding, which have a median size of ~300bp but are only present in half of all islands. Their constitutively unmethylated state is a hallmark of untransformed cells but their increased methylation is a specific and predictive feature of cancer. This study quantifies the two principal mechanisms governing methylation patterns in mammalian genomes. It provides a framework to interpret methylation data across normal and cancer samples and refines the concept of CpG islands. Libraries of DNA sequences were constructed either by mouse genome (129S6) or E.coli genome (NC_010473.1) subrepresentation or custom synthesis. DNA fragments were inserted into the genome of mouse embryonic stem cells by recombination mediated casette exchange (RMCE) at the B-globin locus. Methylation status of the inserted DNA sequences was profiled by bisulfite sequencing using a pair of universal primers flanking the fragments.
2014-09-30 | E-GEOD-51170 | biostudies-arrayexpress
Project description:Unique cell-type specific patterns of DNA methylation in the root meristem
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