Methylome analysis of deoxyadenosines in higher eukaryotes
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ABSTRACT:
PROVIDER: PRJNA299278 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our methylome analysis revealed that dA6m is widely distributed across the eukaryotic genome, and it is present in different cell types. dA6m is commonly depleted in gene exons, whilst it remains abundant in introns. Finally, we have identified the putative consensus sequence, where there is preferential methylation. Since dA6m is a direct modification of DNA, it has the potential to generate a significant impact on different biological areas. Ultimately, our work shows that deoxycytidine modifications might not be the only ones in higher eukaryotes, suggesting that DNA alterations might be more widespread than previously thought.
2015-11-12 | GSE74184 | GEO
Project description:Since the discovery that cytosine deoxynucleotides could be methylated (dC5m), not much is known in higher eukaryotes about modifications affecting other deoxynucleotides. Here, we now report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and human. Our methylome analysis revealed that dA6m is widely distributed across the eukaryotic genome, is present in different cell types, but commonly depleted from gene exons. Since dA6m is a direct modification of DNA, it has the potential to generate a significant impact on different biological areas. Ultimately, our work shows that deoxycytidine modifications might not be the only ones in higher eukaryotes, suggesting that such direct DNA modifications might be more widespread than previously thought.
2015-11-16 | MTBLS276 | MetaboLights
Project description:This data set was downloaded from MetaboLights (http://www.ebi.ac.uk/metabolights/) accession number MTBLS276 Abstract:"Since the discovery that cytosine deoxynucleotides could be methylated (dC5m), not much is known in higher eukaryotes about modifications affecting other deoxynucleotides. Here, we now report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and human. Our methylome analysis revealed that dA6m is widely distributed across the eukaryotic genome, is present in different cell types, but commonly depleted from gene exons. Since dA6m is a direct modification of DNA, it has the potential to generate a significant impact on different biological areas. Ultimately, our work shows that deoxycytidine modifications might not be the only ones in higher eukaryotes, suggesting that such direct DNA modifications might be more widespread than previously thought."
2018-08-07 | MSV000082792 | GNPS
Project description:Methylome analysis in pituitary neuroendocrine tumors
| PRJEB50807 | ENA
Project description:DNA methylation is a widely conserved epigenetic modification that is established and maintained by the cooperative activity of DNA methyltransferases. While the complement of DNA methyltransferase genes can vary substantially between animal species, whole-genome methylation analyses have suggested that major features of animal methylomes are widely conserved. We have now used genome-scale bisulfite sequencing to analyze the methylome of the desert locust, Schistocerca gregaria, which represents an economically important pest with a high degree of phenotypic plasticity. Interestingly, in this system, DNA methylation appears to be both established and maintained by Dnmt1 methyltransferases, which distinguishes locusts from most other known organisms. Our results indicate that the S. gregaria methylome shares preferential methylation of CpG dinucleotides and exons with other animal methylomes. In contrast to other invertebrates, however, overall methylation levels were substantially higher and a significant fraction of transposons was methylated. Additionally, genes were densely methylated in a pronounced bimodal pattern, suggesting a role for DNA methylation in the regulation of locust gene expression. Altogether, our results uncover a unique pattern of genome methylation in locusts and also suggest that animal methylomes may be more diverse than previously thought. Whole exome methylation analysis of S. gregaria. Two samples were analyzed, one sample containing DNA from brain, one sample containing DNA from MTG. To date, there exists no sequenced genome of Schistocerca gregaria; thus, we could only map the data against an EST database (Locust2 EST project) representing the coding part of the genome.
2013-05-03 | E-GEOD-41214 | biostudies-arrayexpress
Project description:DNA methylation is critical for development and is strongly associated with gene regulation. Variation in the DNA methylome between closely related species may reveal unique functional adaptation. We have implemented a novel inter-primate DNA methylation genome-wide analysis between human, chimpanzee and rhesus macaque to identify human species-specific Differentially Methylated Regions (human s-DMRs) in orthologous loci. We analysed the peripheral blood cell DNA methylomes of these primates and identified 22,758 hypomethylated and 15,858 hypermethylated human s-DMRs. These s-DMRs are globally enriched within weak promoter, enhancer and transcribed regions via comparison with ChromHMM segmentation. Human s-DMRs, (both hypo- and hypermethylated) are found to be more prevalent in CpG Island shores than within the islands themselves (?2 P = 1.80 x 10-32). Examining human-specific Transcription Factor Binding Site motif change within CpG islands, we show gain and loss, in hypomethylated and hypermethylated s-DMRs, respectively, of CTCF motifs. Epigenetically the most divergent human-specific locus was the immunological Leukotriene B4 receptor (LTB4R, aka BLT1 receptor), due to collocating hypomethylated s-DMRs within the promoter CpG island and shore, as well as inverse increased gene body methylation. This gene is vital in host immune responses and associated with the pathogenesis of a wide range of human inflammatory diseases. This finding was supported by additional neutrophil-only DNA methylome and lymphoblastoid H3K4me3 chromatin comparative data. Functional investigation of the consequences of these epigenetic differences identified this receptor to have increased expression, and have a higher response to the LTB4 ligand in human versus rhesus macaque peripheral blood mononuclear cells. This result further emphasises the exclusive nature of the human immunological system, its divergent adaptation even from closely related primates, and the power of comparative epigenomics to identify and understand human uniqueness. DNA methylome analysis of pooled Human, Chimpanzee and Macaque
2014-02-01 | E-GEOD-48942 | biostudies-arrayexpress
Project description:Whole methylome analysis of SEM cell lines
| PRJNA433776 | ENA
Project description:Methylome analysis of root-to-shoot transdifferentiation
| PRJNA329116 | ENA
Project description:Aberrant DNA methylation (DNAm) was first linked to cancer over 25 years ago. Since then, many studies have associated hypermethylation of tumour suppressor genes and hypomethylation of oncogenes to the tumourigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs). Recently, new technologies for whole-genome DNAm (methylome) analysis have been developed, enabling unbiased analysis of cancer methylomes. Using MeDIP-seq, we report a sequencing-based comparative methylome analysis of malignant peripheral nerve sheath tumours (MPNST), benign Neurofibromas and normal Schwann cells. Analysis of these methylomes revealed a complex landscape of DNAm alterations. Contrary to the current dogma, significant global hypomethylation was not observed in the MPNST methylome. However, a highly significant (P<10-100) directional difference in DNAm was found in satellite repeats, suggesting these repeats to be the main target for hypomethylation in MPNST. Comparative analysis of the MPNST and Schwann cell methylomes identified 101,466 cancer-associated differentially methylated regions (cDMRs). Analysis showed these cDMRs to be significantly enriched for two satellite repeat types (SATR1 and ARLM-NM-1) and suggests an association between aberrant DNAm of these sequences and transition from healthy cells to malignant disease. Significant enrichment of hypermethylated cDMRs in CGI shores (P<10-60), non-CGI-associated promoters (P<10-4) and hypomethylated cDMRs in SINE repeats (P<10-100) was also identified. Integration of DNAm and gene expression data showed that the expression pattern of genes associated with CGI shore cDMRs was able to discriminate between disease phenotypes. This study establishes MeDIP-seq as an effective method to analyse cancer methylomes. Examination of methylation profiles in malignant, benign and normal tissue
2011-01-01 | E-GEOD-21714 | biostudies-arrayexpress
Project description:Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints. DNA methylation, RNA and nucleosome sequencing data for diverse eukaryotes
2014-03-13 | E-GEOD-46692 | biostudies-arrayexpress