methylMnM

methylMnM integrates MeDIP-seq and MRE-seq data using a joint statistical framework to detect differentially methylated regions and compare whole methylomes.

Key Features:

• Integration of MeDIP-seq and MRE-seq Data: Implements the M&M statistical framework to dynamically scale, normalize, and combine MeDIP-seq and MRE-seq signals for joint analysis.
• Detection of Differentially Methylated Regions: Identifies differentially methylated regions (DMRs) by leveraging combined MeDIP-seq and MRE-seq information.
• Validation against WGBS: Uses sample-matched whole-genome bisulfite sequencing (WGBS) as a gold standard to assess accuracy and reproducibility relative to MeDIP-seq-only methods.
• Cost-effective Comparative Analysis: Leverages the complementary nature of MeDIP-seq and MRE-seq to enable comparative whole-methylome analyses at reduced cost versus WGBS.
• Epigenetic Diversity Characterization: Reveals distinct DNA methylation patterns across tissues, cell types, and individuals.
• Enhancer and Promoter Methylation Insights: Identifies differential methylation at enhancer elements and promoters and reports associations with histone modifications and transcription factor binding.

Scientific Applications:

• X chromosome inactivation: Analysis of DNA methylation patterns relevant to X chromosome inactivation.
• Transposable element repression: Study of methylation involved in transposable element repression.
• Genomic imprinting: Investigation of methylation signatures associated with genomic imprinting.
• Tissue-specific gene expression: Examination of promoter and enhancer methylation underlying tissue-specific gene expression.
• Phenotypic diversity and disease-associated methylation: Comparative methylome analyses to investigate molecular mechanisms underlying phenotypic diversity and disease states associated with aberrant methylation patterns.

Methodology:

Applies the M&M statistical framework to dynamically scale, normalize, and combine MeDIP-seq and MRE-seq data for DMR detection and validates results against sample-matched whole-genome bisulfite sequencing (WGBS).