Repressive Cytosine Methylation is a marker of Viral Gene Transfer across distant eukaryotes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1214807 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have had roles in both transposable element silencing and host gene regulation. To further explore these claims, in this study, we reevaluate the evolutionary origins of DNA methyltransferases and characterise the roles of cytosine methylation on underexplored lineages, including the amoebozoan Acanthamoeba castellanii, the glaucophyte Cyanophora paradoxa, and the heterolobosean Naegleria gruberi. Our analysis of DNA methyltransferase evolution reveals a complex ancestral eukaryotic repertoire, with several eukaryotic lineages encoding enzymes likely acquired through lateral gene transfer (LGT). In the three species examined, DNA methylation is enriched on young transposable elements and silenced genes, suggesting an ancestral repressive function, without the transcriptionally linked gene body methylation of plants and animals. Notably, the closest homologues of many of the silenced, methylated genes in diverse eukaryotes belong to viruses, including giant viruses. Given the widespread occurrence of this pattern across diverse eukaryotic groups, we propose that cytosine methylation was a mechanism originally acquired from bacterial donors to mitigate the expression of both transposable and viral elements, and that this function may persist in creating a permissive atmosphere for LGT in diverse eukaryotic lineages. These findings further highlight the importance of epigenetic information to annotate eukaryotic genomes, as it helps delimit potentially functional LGTs from silenced parasitic elements, less likely to be actively contributing to organism adaptations.
2025-07-28 | GSE287846 | GEO
Project description:DNA methylation is a key mechanism for regulation of DNA repair, DNA replication, and gene expression. In bacteria, DNA is modified by methylation on C5-cytosine (5mC), N6-adenine (6mA) and N4-cytosine (4mC). Metazoans were thought to only use 5mC to regulate gene expression until the recent discovery of N6-adenine methylation in DNA of diverse metazoan species, including mammals. Here we show by dot blot, immunoprecipitation with 4mC-specific antibodies, and ultra-high performance liquid chromatography coupled with triple-quadrupole mass spectrometry that 4mC also occurs in most eukaryotes. We further characterize 4mC sites on a near genome-wide scale by single molecule real time (SMRT) sequencing in the nematode C. elegans. In C. elegans, 4mC is found in all chromosomes but is relatively sparse on the X chromosome. 4mC is relatively enriched on introns, depleted on exons, and co-localizes with 6mA. In human cells, 4mC is anti-correlated with 5mC. Moreover, 4mC modifications are associated with increased gene expression. Transfection of human cells with a 4mC-modified luciferase reporter plasmid increases luciferase expression as compared to the unmethylated plasmid. These data suggest that 4mC promotes gene transcription, playing an opposing role to 5mC, which generally represses transcription. Thus 4mC modification of DNA is a previously unrecognized mechanism of gene regulation in eukaryotes, providing evidence for a complex epigenetic DNA code.
2018-09-01 | GSE86993 | 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:Transposable elements are entangled in a constant evolutionary arms race with their host genomes, constantly evolving ways to evade host silencing mechanisms. One silencing mechanism used by many distantly related eukaryotes is dependent on cytosine methylation, an epigenetic mark deposited by C5 cytosine methyltransferases (CMTs). Therefore, it is expected transposable elements would acquire mechanisms to escape from being targeted by cytosine methylation. Here we report how two distantly related eukaryotic lineages have incorporated CMTs into the coding regions of distinct retrotransposon classes. Three of these events have occurred in the dinoflagellates of the genus Symbiodinium, where these CMT-encoding retrotransposons show hundreds of insertions. In a case of convergent evolution, the charophyte Klebsormidium nitens shows an independent expansion of CMT encoding retrotransposons. Concomitantly, we find that Symbiodinium genomes show cytosine methylation patterns unlike any other eukaryote with most of the genome hypermethylated in CpGs, while targeted CH methylation accumulates on transposable elements. Similarly, K. nitens shows CHH and CHG targeted methylation on repressed transposable elements, while CpG methylation is concentrated in gene bodies and transposable elements. Furthermore, we demonstrate the ability of retrotransposon CMTs to de novo methylate CpGs, indicating a putative role in mimicking retrotranscribed DNA as host active genomic DNA. Our results show an unprecedented example of how retrotransposons incorporate host-derived genes involved in DNA methylation as a source of adaptation to their host epigenomic environments.
2018-04-11 | GSE104474 | GEO
Project description:DNA methylation (5mC) plays important roles in epigenetic regulation of genome function, and recently the TET1-3 hydroxylases have been found to oxidize 5mC to hydroxymethylcytosine (5hmC), formylcytosine (5fC), and carboxylcytosine (5caC) in DNA. These derivatives have a role in demethylation of DNA but in addition may have epigenetic signaling functions in their own right. A recent study identified proteins with preferential binding to 5-methylcytosine (5mC) and its oxidized forms where readers for 5mC and 5hmC (5-hydroxymethylcytosine) showed little overlap while further oxidation forms enriched for repair proteins and transcription regulators. We extend this study by using promoter sequences as baits and compare protein binding patterns to unmodified or modified cytosine containing DNA using mouse embryonic stem cell (mESCs) extracts. The dataset contains 3 biological replicates each of mouse ES cell nuclear proteins binding to Pax6 and FGF15 promoter sequences containing different modified forms of cytosine. Data analysis: Mass spectrometric data were processed using Proteome Discoverer v1.3 and searched against a mammalian entries in Uniprot 2011.09 using Mascot v2.3 with the following parameters: Enzyme - trypsin; max 1 missed cleavage; Precursor Mass Tolerance - 10 ppm; Fragment Mass Tolerance - 0.6 Da; Dynamic Modification - Oxidation (M); Static Modification - Carbamidomethyl at C.
2013-10-21 | PXD000524 | Pride
Project description:Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals and plants. The composition, biochemistry, and developmental function of PRC2 in animal and flowering plant model species are relatively well described. Recent evidence demonstrates the presence of PRC2 complexes in various eukaryotic supergroups, suggesting conservation of the complex and its function. Here, we provide an overview of the current understanding of PRC2-mediated repression in different representatives of eukaryotic supergroups with a focus on the green lineage. By comparison of PRC2 in different eukaryotes, we highlight the possible common and diverged features suggesting evolutionary implications and outline emerging questions and directions for future research of polycomb repression and its evolution.
| S-EPMC8788455 | biostudies-literature
Project description:To gain a more depth knowledge of repressive epigenetic gene regulation in UCC, we have profiled H3K9m3 and H3K27m3 in normal and malignant urothelial cells. We matched these profiles to those 5-methylcytosine and gene expression. We hypothesized that differences represent pro-carcinogenic events within the urothelium. We identified a panel of genes with cancer specific epigenetic mediated aberrant expression. Two repressive histone modifications (H3K9m3 and H3K27m3) , cytosine methylation and gene expression were compared between normal human urothelial cell line (NHU) and malignant urothelial cells (EJ and RT112).
2011-09-19 | E-GEOD-31864 | biostudies-arrayexpress
Project description:Estimating diversity of Baltic Sea ice eukaryotes
| PRJEB7625 | ENA