ArticleNucleic acids research2019
Analyzing whole genome bisulfite sequencing data from highly divergent genotypes.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Non-Mendelian inheritance of DNA methylation patterns in mice.Nature genetics · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Unnatural Cytosine Analogs Potentiate a Customizable, Enzymatic Method for Integrated Epigenetic and Four-Base Genetic Sequencing.Journal of the American Chemical Society · 2026Article
- BenchmarkingInternational journal of molecular sciences · 2026Article
- Insights into natural neocentromere evolution from a cattle T2T X chromosome.Nature communications · 2025Article
- Phased epigenomics and methylation inheritance in a historical Vitis vinifera hybrid.Genome biology · 2025Article
- Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA.Genome research · 2025Article
- When less is more: sketching with minimizers in genomics.Genome biology · 2024Review
- DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era.GigaScience · 2024Article
- Precision pharmacological reversal of strain-specific diet-induced metabolic syndrome in mice informed by epigenetic and transcriptional regulation.PLoS genetics · 2023Article
- Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii.Plant physiology · 2023Article
- High Nucleotide Diversity Accompanies Differential DNA Methylation in Naturally Diverging Populations.Molecular biology and evolution · 2023Article
- Article
- The Chromatin Remodeling FactorPlants (Basel, Switzerland) · 2023Article
- Phenotypic and Methylome Responses to Salt Stress inFrontiers in plant science · 2022Article
- Antioxidant Regulation and DNA Methylation Dynamics DuringFrontiers in plant science · 2022Article
- Introduction to Single-Cell DNA Methylation Profiling Methods.Biomolecules · 2021Review
- Genome-wide detection of cytosine methylation by single molecule real-time sequencing.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Evolutionary and functional genomics of DNA methylation in maize domestication and improvement.Nature communications · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
In the study of DNA methylation, genetic variation between species, strains or individuals can result in CpG sites that are exclusive to a subset of samples, and insertions and deletions can rearrange the spatial distribution of CpGs. How to account for this variation in an analysis of the interplay between sequence variation and DNA methylation is not well understood, especially when the number of CpG differences between samples is large. Here, we use whole-genome bisulfite sequencing data on two highly divergent mouse strains to study this problem. We show that alignment to personal genomes is necessary for valid methylation quantification. We introduce a method for including strain-specific CpGs in differential analysis, and show that this increases power. We apply our method to a human normal-cancer dataset, and show this improves accuracy and power, illustrating the broad applicability of our approach. Our method uses smoothing to impute methylation levels at strain-specific sites, thereby allowing strain-specific CpGs to contribute to the analysis, while accounting for differences in the spatial occurrences of CpGs. Our results have implications for joint analysis of genetic variation and DNA methylation using bisulfite-converted DNA, and unlocks the use of personal genomes for addressing this question.
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Registered trials
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