ArticleBMC bioinformatics2020
MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Linking STRs/SNPs and DNA methylation using massively parallel sequencing for potential forensic applications.International journal of legal medicine · 2026Article
- Expanding Upon Genomics in Rare Diseases: Epigenomic Insights.International journal of molecular sciences · 2024Review
- bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data.BMC bioinformatics · 2024Article
- Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing.Nucleic acids research · 2024Article
- ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms.Nucleic acids research · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundDNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms. Parental alleles in haploid genomes may exhibit different methylation patterns, which can lead to different phenotypes and even different therapeutic and drug responses to diseases. However, to our knowledge, no software is available for the identification of DNA methylation haplotype regions with combined allele-specific DNA methylation, single nucleotide polymorphisms (SNPs) and high-throughput chromosome conformation capture (Hi-C) data.
resultsIn this paper, we developed a new method, MethHaplo, that identify DNA methylation haplotype regions with allele-specific DNA methylation and SNPs from whole-genome bisulfite sequencing (WGBS) data. Our results showed that methylation haplotype regions were ten times longer than haplotypes with SNPs only. When we integrate WGBS and Hi-C data, MethHaplo could call even longer haplotypes.
conclusionsThis study illustrates the usefulness of methylation haplotypes. By constructing methylation haplotypes for various cell lines, we provide a clearer picture of the effect of DNA methylation on gene expression, histone modification and three-dimensional chromosome structure at the haplotype level. Our method could benefit the study of parental inheritance-related disease and hybrid vigor in agriculture.
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