ArticleBMC genomics2019
Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
95 citing papers in PubMed, 183 citations in OpenAlex.
- Epigenetics in development, disease, and therapy: from mechanisms to clinical interventions.Science China. Life sciences · 2026Review
- DNA Adenine Methylation Clock in Brain Aging and Alzheimer's Disease Progression.bioRxiv : the preprint server for biology · 2026Article
- EnDeep4mC predicts DNAGenome research · 2026Article
- Metabolic isotopic labeling of (deoxy)ribose enables dual neutral loss scanning for profiling nucleic acid modifications.Nucleic acids research · 2026Article
- Article
- Dual genomic localizations and gene regulatory functions of MBD-2 with and without NuRD in Caenorhabditis elegans which lacks DNA methylation.Nature communications · 2026Article
- A PIWI protein-dependent DNA N6-adenine methylation pathway inbioRxiv : the preprint server for biology · 2026Article
- Prediction of DNA N4-Methylcytosine Sites Based on a Position-Aligned Multi-branch Fusion Network.Computational and structural biotechnology journal · 2026Article
- Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes.Nature genetics · 2025Article
- iDNA-DAPHA: a generic framework for methylation prediction via domain-adaptive pretraining and hierarchical attention.Briefings in bioinformatics · 2025Article
- Article
- Distribution patterns of N6-methyladenine in the rye genome.Scientific reports · 2025Article
- Direct single-nucleotide resolution sequencing of DNA 5-methylcytosine using engineered DNA methyltransferase-mediated CMD-seq.Chemical science · 2025Article
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 2025Article
- Comprehensive comparison of the third-generation sequencing tools for bacterial 6mA profiling.Nature communications · 2025Article
- Review
- Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis.Communications biology · 2025Article
- Structure-Activity Relationship Studies of DNA Methyltransferase 1 Monovalent Degraders.Journal of medicinal chemistry · 2025Article
- Mapping epigenetic modifications by sequencing technologies.Cell death and differentiation · 2025Review
- Host RNA NMolecular therapy : the journal of the American Society of Gene Therapy · 2024Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundDirected DNA methylation on N6-adenine (6mA), N4-cytosine (4mC), and C5-cytosine (5mC) can potentially increase DNA coding capacity and regulate a variety of biological functions. These modifications are relatively abundant in bacteria, occurring in about a percent of all bases of most bacteria. Until recently, 5mC and its oxidized derivatives were thought to be the only directed DNA methylation events in metazoa. New and more sensitive detection techniques (ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-ms/ms) and single molecule real-time sequencing (SMRTseq)) have suggested that 6mA and 4mC modifications could be present in a variety of metazoa.
resultsHere, we find that both of these techniques are prone to inaccuracies, which overestimate DNA methylation concentrations in metazoan genomic DNA. Artifacts can arise from methylated bacterial DNA contamination of enzyme preparations used to digest DNA and contaminating bacterial DNA in eukaryotic DNA preparations. Moreover, DNA sonication introduces a novel modified base from 5mC that has a retention time near 4mC that can be confused with 4mC. Our analyses also suggest that SMRTseq systematically overestimates 4mC in prokaryotic and eukaryotic DNA and 6mA in DNA samples in which it is rare. Using UHPLC-ms/ms designed to minimize and subtract artifacts, we find low to undetectable levels of 4mC and 6mA in genomes of representative worms, insects, amphibians, birds, rodents and primates under normal growth conditions. We also find that mammalian cells incorporate exogenous methylated nucleosides into their genome, suggesting that a portion of 6mA modifications could derive from incorporation of nucleosides from bacteria in food or microbiota. However, gDNA samples from gnotobiotic mouse tissues found rare (0.9-3.7 ppm) 6mA modifications above background.
conclusionsAltogether these data demonstrate that 6mA and 4mC are rarer in metazoa than previously reported, and highlight the importance of careful sample preparation and measurement, and need for more accurate sequencing techniques.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.