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Global analysis of cytosine and adenine DNA modifications across the tree of life

https://doi.org/10.7554/elife.81002
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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5‐Hydroxymethylcytosine, the Sixth Base of the Genome
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Recent Advances in the Genomic Profiling of Bacterial Epigenetic Modifications
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Using ggtree to Visualize Data on Tree‐Like Structures
inferredcites →https://doi.org/10.1007/978-3-319-43624-1_10openalex-snapshot
N6-Methyladenine: A Conserved and Dynamic DNA Mark
inferredcites →https://doi.org/10.1007/978-94-007-4525-4_13openalex-snapshot
The Role of DNA Methylation and Histone Modifications in Transcriptional Regulation in Humans
inferredcites →https://doi.org/10.1007/s11357-018-0005-3openalex-snapshot
Analysis of DNA modifications in aging research
inferredcites →https://doi.org/10.1016/0014-5793(83)80745-5openalex-snapshot
Cytosine modification in DNA by BcnI methylase yields N4‐methylcytosine
inferredcites →https://doi.org/10.1016/b978-0-12-801596-4.00006-xopenalex-snapshot
DNA Modifications and Memory
inferredcites →https://doi.org/10.1016/j.ab.2011.01.026openalex-snapshot
A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples
inferredcites →https://doi.org/10.1016/j.cell.2015.04.018openalex-snapshot
N6-Methyladenine DNA Modification in Drosophila
inferredcites →https://doi.org/10.1016/j.csbj.2020.03.010openalex-snapshot
Mapping and editing of nucleic acid modifications
inferredcites →https://doi.org/10.1016/j.devcel.2018.03.012openalex-snapshot
DNA N-Adenine Methylation in Arabidopsis thaliana
inferredcites →https://doi.org/10.1016/j.ijmm.2006.10.002openalex-snapshot
DNA adenine methylation and bacterial pathogenesis
inferredcites →https://doi.org/10.1016/j.jchromb.2014.01.050openalex-snapshot
A validated quantitative liquid chromatography–tandem quadrupole mass spectrometry method for monitoring isotopologues to evaluate global modified cytosine ratios in genomic DNA
inferredcites →https://doi.org/10.1016/s0021-9258(18)57261-6openalex-snapshot
THE QUANTITATIVE SEPARATION OF PURINES, PYRIMIDINES, AND NUCLEOSIDES BY PAPER CHROMATOGRAPHY
inferredcites →https://doi.org/10.1021/ac500447wopenalex-snapshot
Cytosine DNA Methylation Is Found in Drosophila melanogaster but Absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Other Yeast Species
inferredcites →https://doi.org/10.1021/ac504786ropenalex-snapshot
Sensitive and Simultaneous Determination of 5-Methylcytosine and Its Oxidation Products in Genomic DNA by Chemical Derivatization Coupled with Liquid Chromatography-Tandem Mass Spectrometry Analysis
inferredcites →https://doi.org/10.1038/175336a0openalex-snapshot
Occurrence of a New Base in the Deoxyribonucleic Acid of a Strain of Bacterium Coli
inferredcites →https://doi.org/10.1038/35046205openalex-snapshot
DNA methylation in Drosophila melanogaster
inferredcites →https://doi.org/10.1038/nn.2666openalex-snapshot
DNA methylation and memory formation
inferredcites →https://doi.org/10.1038/nn.2900openalex-snapshot
Neuronal activity modifies the DNA methylation landscape in the adult brain
inferredcites →https://doi.org/10.1038/nrg3354openalex-snapshot
DNA methylation: roles in mammalian development
inferredcites →https://doi.org/10.1038/s41586-020-2119-xopenalex-snapshot
Spatiotemporal DNA methylome dynamics of the developing mouse fetus
inferredcites →https://doi.org/10.1038/s41598-019-41070-yopenalex-snapshot
Tracking Decitabine Incorporation into Malignant Myeloid Cell DNA in vitro and in vivo by LC-MS/MS with Enzymatic Digestion
inferredcites →https://doi.org/10.1042/bj20140844openalex-snapshot
Trace analysis of methylated and hydroxymethylated cytosines in DNA by isotope-dilution LC–MS/MS: first evidence of DNA methylation in Caenorhabditis elegans
inferredcites →https://doi.org/10.1073/pnas.1109631108openalex-snapshot
DNA methylation regulates phenotype-dependent transcriptional activity in Candida albicans
inferredcites →https://doi.org/10.1080/00275514.1998.12026971openalex-snapshot
A Comparison of DNA Methylation Levels in Selected Isolates of Higher Fungi
inferredcites →https://doi.org/10.1080/15592294.2017.1411447openalex-snapshot
Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements
inferredcites →https://doi.org/10.1089/ars.2012.4923openalex-snapshot
Deciphering the Epigenetic Code: An Overview of DNA Methylation Analysis Methods
inferredcites →https://doi.org/10.1093/nar/gky879openalex-snapshot
BacDivein 2019: bacterial phenotypic data for High-throughput biodiversity analysis
inferredcites →https://doi.org/10.1093/nass/2.1.73openalex-snapshot
N4,5-dimethylcytosine, a novel hypermodified base in DNA
inferredcites →https://doi.org/10.1101/2020.04.09.033167openalex-snapshot
Origin and Evolution of DNA methyltransferases (DNMT) along the tree of life: A multi-genome survey
inferredcites →https://doi.org/10.1101/gr.257576.119openalex-snapshot
Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
inferredcites →https://doi.org/10.1111/1755-0998.12244openalex-snapshot
Application of the LU minometric M ethylation A ssay to ecological species: tissue quality requirements and a survey of DNA methylation levels in animals
inferredcites →https://doi.org/10.1126/science.1169786openalex-snapshot
The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain
inferredcites →https://doi.org/10.1126/science.1170116openalex-snapshot
Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
inferredcites →https://doi.org/10.1126/science.1210597openalex-snapshot
Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine
inferredcites →https://doi.org/10.1126/science.264.5157.421openalex-snapshot
Stomatal Size in Fossil Plants: Evidence for Polyploidy in Majority of Angiosperms
inferredcites →https://doi.org/10.1126/science.abe7489openalex-snapshot
Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution
inferredcites →https://doi.org/10.1128/jb.169.3.939-943.1987openalex-snapshot
N4-methylcytosine as a minor base in bacterial DNA
inferredcites →https://doi.org/10.1186/1756-8935-2-7openalex-snapshot
Tissue-specific variation in DNA methylation levels along human chromosome 1
inferredcites →https://doi.org/10.1186/s12864-019-5754-6openalex-snapshot
Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA
inferredcites →https://doi.org/10.1186/s13036-017-0052-9openalex-snapshot
Technical advances in global DNA methylation analysis in human cancers
inferredcites →https://doi.org/10.1186/s13072-015-0016-6openalex-snapshot
Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond
inferredcites →https://doi.org/10.1186/s13075-019-1936-5openalex-snapshot
Higher baseline global leukocyte DNA methylation is associated with MTX non-response in early RA patients
inferredcites →https://doi.org/10.1371/journal.pone.0015367openalex-snapshot
Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates
inferredcites →https://doi.org/10.17632/jnbn8c2phvopenalex-snapshot
Supplementary Information for sample sources: Global analysis of cytosine and adenine DNA modifications across the tree of life
inferredcites →https://doi.org/10.3389/fcell.2018.00024openalex-snapshot
A Lexicon of DNA Modifications: Their Roles in Embryo Development and the Germline
inferredcites →https://doi.org/10.3389/fcell.2018.00027openalex-snapshot
Developmental Functions of the Dynamic DNA Methylome and Hydroxymethylome in the Mouse and Zebrafish: Similarities and Differences
inferredcites →https://doi.org/10.3389/fmicb.2018.00137openalex-snapshot
The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius
inferredcites →https://doi.org/10.3389/fmicb.2020.616922openalex-snapshot
Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns
inferredcites →https://doi.org/10.3389/fonc.2019.00194openalex-snapshot
Epigenetic Enzyme Mutations: Role in Tumorigenesis and Molecular Inhibitors
inferredcites →https://doi.org/10.3390/genes11010110openalex-snapshot
Understanding the Relevance of DNA Methylation Changes in Immune Differentiation and Disease
inferredcites →https://doi.org/10.3934/genet.2019.4.70openalex-snapshot
Evidence for novel epigenetic marks within plants
inferredcites →https://doi.org/10.7554/elife.81002openalex-snapshot
Global analysis of cytosine and adenine DNA modifications across the tree of life

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4643724openalex-extracted
Synthesis and Anti-Cancer Investigations of Novel Copper(II) Complexes Based on Adenine
inferred← citeshttps://doi.org/10.1002/bies.202200232openalex-snapshot
Shaping eukaryotic epigenetic systems by horizontal gene transfer
inferred← citeshttps://doi.org/10.1016/b978-0-12-814809-9.00009-3openalex-snapshot
Chromatin and transcription
inferred← citeshttps://doi.org/10.1016/j.molstruc.2024.138836openalex-snapshot
Synthesis and anti-cancer investigations of copper(II) complexes based on adenine
inferred← citeshttps://doi.org/10.1038/s41586-025-09205-6openalex-snapshot
The role of metabolism in shaping enzyme structures over 400 million years
inferred← citeshttps://doi.org/10.1093/gigascience/giaf014openalex-snapshot
Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)
inferred← citeshttps://doi.org/10.1101/2023.11.04.565605openalex-snapshot
Probing the Evolution of Genes Associated With DNA Methylation in Listeria monocytogenes
inferred← citeshttps://doi.org/10.1101/2025.06.20.660749openalex-snapshot
Epigenetic age prediction using N6-methyladenine in the bumblebee Bombus terrestris
inferred← citeshttps://doi.org/10.1101/gr.277743.123openalex-snapshot
Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
inferred← citeshttps://doi.org/10.1101/gr.278661.123openalex-snapshot
Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer ( Ostrinia furnacalis )
inferred← citeshttps://doi.org/10.1111/acel.70312openalex-snapshot
Epigenetic Age Prediction Using N 6‐Methyladenine in the Buff‐Tailed Bumblebee ( Bombus terrestris )
inferred← citeshttps://doi.org/10.1111/eva.13730openalex-snapshot
The evolutionary consequences of interactions between the epigenome, the genome and the environment
inferred← citeshttps://doi.org/10.3389/fmolb.2025.1681568openalex-snapshot
Global DNA-methylation in quantitative epigenetics: orbitrap mass spectrometry
inferred← citeshttps://doi.org/10.3389/fpls.2023.1278185openalex-snapshot
The role of epigenetic and epitranscriptomic modifications in plants exposed to non-essential metals
inferred← citeshttps://doi.org/10.3390/biology14050461openalex-snapshot
Cross-Kingdom DNA Methylation Dynamics: Comparative Mechanisms of 5mC/6mA Regulation and Their Implications in Epigenetic Disorders
inferred← citeshttps://doi.org/10.3390/dna5020019openalex-snapshot
Chemical Versus Enzymatic Nucleic Acid Modifications and Genomic Stability
inferred← citeshttps://doi.org/10.3390/ijms232113495openalex-snapshot
Light Dependent Changes in Adenylate Methylation of the Promoter of the Mitochondrial Citrate Synthase Gene in Maize (Zea mays L.) Leaves
inferred← citeshttps://doi.org/10.3390/ijms241914746openalex-snapshot
Base Excision DNA Repair in Plants: Arabidopsis and Beyond
inferred← citeshttps://doi.org/10.3390/ijms25020686openalex-snapshot
Structural Basis of Nucleic Acid Recognition and 6mA Demethylation by Caenorhabditis elegans NMAD-1A
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