ArticleScientific reports2019
Universality of the DNA methylation codes in Eucaryotes.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Multiomics Reveal Associations Between CpG Methylation, Histone Modifications and Transcription in a Species That has Lost DNMT3, the Colorado Potato Beetle.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Article
- Identification of novel H2A histone variants across diverse clades of algae.Genome biology · 2025Article
- The Genome Architecture of the Copepod Eurytemora carolleeae - the Highly Invasive Atlantic Clade of the Eurytemoraaffinis Species Complex.Genomics, proteomics & bioinformatics · 2024Article
- An epigenetic toolbox for conservation biologists.Evolutionary applications · 2024Article
- DNA Methylation Machinery in Gastropod Mollusks.Life (Basel, Switzerland) · 2024Review
- Hypermethylation of the CTRP9 promoter region promotes Hcy induced VSMC lipid deposition and foam cell formation via negatively regulating ER stress.Scientific reports · 2023Article
- Review
- Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases.eLife · 2023Article
- Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases.bioRxiv : the preprint server for biology · 2023Article
- InvestigatingInternational journal of molecular sciences · 2023Review
- Epigenetic machinery is functionally conserved in cephalopods.BMC biology · 2022Article
- A Broad Survey of Gene Body and Repeat Methylation in Cnidaria Reveals a Complex Evolutionary History.Genome biology and evolution · 2022Article
- Evolution of DNA Methylation Across Ecdysozoa.Journal of molecular evolution · 2022Article
- The Long and Short of Next Generation Sequencing forFrontiers in cellular and infection microbiology · 2022Review
- The methylome of Biomphalaria glabrata and other mollusks: enduring modification of epigenetic landscape and phenotypic traits by a new DNA methylation inhibitor.Epigenetics & chromatin · 2021Article
- DNA methylation atlas and machinery in the developing and regenerating annelid Platynereis dumerilii.BMC biology · 2021Article
- Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress.Scientific reports · 2021Article
- Inference of DNA methylation patterns in molluscs.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Article
- Review
- DNA methyltransferase 3a mediates developmental thermal plasticity.BMC biology · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genetics and epigenetics are tightly linked heritable information classes. Question arises if epigenetics provides just a set of environment dependent instructions, or whether it is integral part of an inheritance system. We argued that in the latter case the epigenetic code should share the universality quality of the genetic code. We focused on DNA methylation. Since availability of DNA methylation data is biased towards model organisms we developed a method that uses kernel density estimations of CpG observed/expected ratios to infer DNA methylation types in any genome. We show here that our method allows for robust prediction of mosaic and full gene body methylation with a PPV of 1 and 0.87, respectively. We used this prediction to complement experimental data, and applied hierarchical clustering to identify methylation types in ~150 eucaryotic species covering different body plans, reproduction types and living conditions. Our analysis indicates that there are only four gene body methylation types. These types do not follow phylogeny (i.e. phylogenetically distant clades can have identical methylation types) but they are consistent within clades. We conclude that the gene body DNA methylation codes have universality similar to the universality of the genetic code and should consequently be considered as part of the inheritance system.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.