MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification
- PDF / 1,702,937 Bytes
- 19 Pages / 595.276 x 790.866 pts Page_size
- 109 Downloads / 186 Views
Open Access
SOFTWARE
MethHaplo: combining allele‑specific DNA methylation and SNPs for haplotype region identification Qiangwei Zhou1,2, Ze Wang3, Jing Li3, Wing‑Kin Sung2,4,5 and Guoliang Li1,2*
*Correspondence: [email protected] 1 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Full list of author information is available at the end of the article
Abstract Background: DNA 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. Results: In 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. Conclusions: This 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 threedimensional chromosome structure at the haplotype level. Our method could benefit the study of parental inheritance-related disease and hybrid vigor in agriculture. Keywords: DNA methylation, Allele-specific DNA methylation, CTCF, SNP, Allelespecific gene expression
Background Genetic variations have vital effects on an organism’s phenotype, which can be studied with haplotypes. Haplotypes can refer to the combinations of alleles or a group of single nucleotide polymorphisms (SNPs) found on the same chromosome [1]. Haplotype analysis has applications in the diagnosis of genetic diseases, ancestry inference, and drug design [2–4]. Generally, the differences in the two haplotypes of an individual’s genome are mainly caused by heterozygous single nucleotide polymorphisms (SNPs) where the haplotypes contain two distinct alleles. In diploid genomes, some parental alleles exhibit different DNA methylation patterns, which may cause variance in individuals with © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article a
Data Loading...
