AUTHOR=Peng Xiaoqing , Li Yiming , Kong Xiangyan , Zhu Xiaoshu , Ding Xiaojun 

TITLE=Investigating Different DNA Methylation Patterns at the Resolution of Methylation Haplotypes

JOURNAL=Frontiers in Genetics

VOLUME=Volume 12 - 2021

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.697279

DOI=10.3389/fgene.2021.697279

ISSN=1664-8021

ABSTRACT=Different DNA methylation patterns presented on different tissues or cell types are considered as one of the main reasons accounting for the tissue-specific gene expressions. In recent years, many methods have been proposed to identify differentially methylated regions (DMRs) based on the mixture of methylation signals from homologous chromosomes.
To investigate the possible influence of homologous chromosomes on methylation analysis, a method, named MHap, is proposed to construct methylation haplotypes for homologous chromosomes in CpG dense regions. Then, a simple method, MHap\_DMR, is developed to identify DMRs based on methylation haplotypes. Through comparing the methylation consistency between homologous chromosomes in different cell types, we found that majority of paired methylation haplotypes derived from homologous chromosomes are consistent, while a lower methylation consistency was observed in the breast cancer sample. We also observed that the hypomethylation consistency of differentiated cells is higher than that of the corresponding undifferentiated stem cells. The methylation haplotype modes of DMRs identified by MHap\_DMR can help to investigate the DNA methylation changing directions of homologous chromosomes in cell differentiation and cancerization. The code is available at https://github.com/xqpeng/MHap\_DMR.