ArticleGenome research2023
Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 14 citations in OpenAlex.
- DNA Hypomethylation Is Not Cell Intrinsically Toxic to Polycomb Repressive Complex 2 Deficient Malignant Peripheral Nerve Sheath Tumors.Genes, chromosomes & cancer · 2026Article
- Gene body methylation suppresses intragenic transcription and permits epigenetic inheritance in a cnidarian.Nature ecology & evolution · 2026Article
- Genome-wide and gene-specific DNA methylation across developmental stages in Pogonomyrmex californicus: A socially polymorphic ant.Insect molecular biology · 2026Article
- Complete mitochondrial genome characterization and exploratory mitochondrial DNA modification signals in square-head catfish Chaca chaca.Scientific reports · 2026Article
- Hypomorphic Protein Expression of DNA Polymerase Beta in PolβBiomolecules · 2026Article
- Genome-wide analysis of strand-specific transcription and DNA methylation inFrontiers in microbiology · 2026Article
- Epigenotoxicity: Decoding the epigenetic imprints of genotoxic agents and their implications for regulatory genetic toxicology.Environmental and molecular mutagenesis · 2025Review
- Computational analysis of DNA methylation from long-read sequencing.Nature reviews. Genetics · 2025Review
- De novo whole-genome assembly of the critically endangered southern muriqui (Brachyteles arachnoides).G3 (Bethesda, Md.) · 2025Article
- Sequencing and assembling the genome of Przewalski's horse in the classroom.Journal of equine veterinary science · 2025Review
- High-Throughput Sequencing Enables Rapid Analyses of Nematode Mitochondrial Genomes from an Environmental Sample.Pathogens (Basel, Switzerland) · 2025Article
- Low-pass nanopore sequencing for measurement of global methylation levels in plants.BMC genomics · 2024Article
- Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria.Genome biology · 2024Article
- Differential usage of DNA modifications in neurons, astrocytes, and microglia.Epigenetics & chromatin · 2023Article
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1 author at 1 institution in 1 country.
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Abstract
Genome skimming is defined as low-pass sequencing below 0.05× coverage and is typically used for mitochondrial genome recovery and species identification. Long-read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001×, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole-genome bisulfite sequencing and an average mapping rate >97%. Genome size directly correlates to global DNA methylation, explaining 39% of its variance. Accurate SINE and LINE transposon methylation in both the mouse and primates can be obtained with just 0.0001× coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology and for low-resource groups.
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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.