MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification

BMC Bioinformatics

Wing-Kin Sung¹  Ze Wang²  Jing Li²  Qiangwei Zhou³  Guoliang Li³ 

[1] Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, 430070, Wuhan, China;Department of Computer Science, National University of Singapore, 117417, Singapore, Singapore;Department of Computational and Systems Biology, Genome Institute of Singapore, 138672, Singapore, Singapore;College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China;National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China;Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, 430070, Wuhan, China;

关键词: DNA methylation;    Allele-specific DNA methylation;    CTCF;    SNP;    Allele-specific gene expression;   

DOI  :  10.1186/s12859-020-03798-7

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY