mHapBrowser: a comprehensive database for visualization and analysis of DNA methylation haplotypes

Area of Science:

• Epigenetics
• Genomics
• Bioinformatics

Background:

• DNA methylation is a key epigenetic regulator of gene expression.
• Bisulfite sequencing provides single-base resolution of methylation.
• Current databases lack analysis of phased methylation patterns (mHaps).

Purpose of the Study:

• Introduce mHapBrowser, a database for visualizing and analyzing DNA methylation haplotypes (mHaps).
• Provide tools for comparing mHap patterns across diverse samples.
• Facilitate downstream analysis of mHap data.

Main Methods:

• Systematic processing of public bisulfite sequencing data from human, mouse, and rat tissues.
• Generation of mHap format files for 6366 samples.
• Integration with WashU Epigenome Browser for visualization and an online server for comparison.

Main Results:

• mHapBrowser enables visualization of eight mHap metrics and comparison across samples.
• Demonstrated association between mHap patterns and gene expression.
• Showcased mHap patterns' role in lung cancer subtype differential expression and improved tumor classification from cell-free DNA.

Conclusions:

• mHapBrowser provides a valuable resource for exploring DNA methylation haplotypes.
• Phased methylation patterns offer insights beyond mean methylation levels.
• mHap analysis has potential applications in gene regulation studies and disease diagnostics.