MethHaplo

MethHaplo identifies DNA methylation haplotype regions by integrating allele-specific DNA methylation and single nucleotide polymorphism (SNP) data from whole-genome bisulfite sequencing (WGBS) to enable haplotype-level analysis of epigenetic variation affecting gene expression, histone modification, and three-dimensional chromosome structure.

Key Features:

• Integration of Epigenetic and Genetic Data: Combines allele-specific DNA methylation patterns with SNPs from WGBS to identify methylation haplotypes and recover longer haplotypes than SNPs alone.
• Incorporation of Hi-C Data: Integrates high-throughput chromosome conformation capture (Hi-C) data to extend identified haplotype regions and relate methylation haplotypes to three-dimensional chromatin organization.
• Methylation Haplotype Construction across Cell Lines: Constructs detailed methylation haplotypes across various cell lines to support analyses of parental inheritance-related diseases, hybrid vigor in agriculture, and associations with therapeutic responses and disease mechanisms.

Scientific Applications:

• Genetic Research: Aids understanding of the genetic basis of complex traits and diseases by identifying longer haplotype regions linking SNPs and methylation.
• Epigenomics: Illuminates the role of DNA methylation in gene regulation and epigenetic modification at the haplotype level.
• Chromatin Architecture Studies: Enables analysis of how methylation haplotypes correlate with three-dimensional chromatin organization using Hi-C integration.
• Disease Research: Supports investigation of parental inheritance-related diseases and therapeutic response mechanisms through haplotype-resolved methylation patterns.
• Agricultural Genetics: Facilitates study of hybrid vigor and epigenetic contributions to phenotypic outcomes in agricultural species.

Methodology:

Combines allele-specific DNA methylation calls with SNP information derived from WGBS and can optionally incorporate Hi-C data to identify extended DNA methylation haplotype regions.